I think you miss a lot of subtleties here.
Yes, the final authorities on all issues are contemporary posekim. This is how it's supposed to be: each community must follow its own leaders in its own generation. This is what we learn from Parshas Shofetim, where the Torah says "ובאת אל הכהנים הלוים ואל השפט אשר יהיה בימים ההם". As Rashi explains ad loc., the Torah says "in those days" to teach us that we must follow the leaders in our generation even if they're lesser than previous generations.
In the time of the Sanhedrin, this was explicit. As with modern legislatures, the ruling of a later Sanhedrin superseded any previous ones. Although the earlier ones were presumably greater -- the members of some were nevi'im -- the later ones had more authority, because they were expected to take into account the earlier rulings and only overturn them for good reason.
This is the key point. Judaism does not operate according to a purely traditional model in which nothing can ever change. But neither does it give complete authority to each generation to do as it will. Each generation's leaders must decide for themselves how to rule, but only as far as they pay great respect to past rulers.
So the correct summary would be that the current posekim are the final authorities. But they must give very great weight to the rulings of the Acharonim, who must give very great weight to the rulings of the Rishonim, etc. In most cases, if the Gemara decides an issue the Rishonim will not overrule it; if a clear majority of Rishonim agree on an issue the Acharonim will not overrule it; and so on.
Now, in every generation you can find plenty of places where earlier generations are actually overruled. But this is part of the system, as long as it's done with great respect and in limited doses. Almost any major posek will overturn at least a few significant precedents. This is true for the modern/rationalist world just as much as for the chareidi world, or probably more so.
An unwritten rule is that when overturning an established ruling, posekim must try to explain how the earlier ruling wasn't really wrong. This can range from saying it wasn't really talking about our situation, to saying it was a copyist's error or forgery or "don't ask questions". The explanation can be elaborate or implausible, but it should be there.
This rule is unwritten, of course, because to write it down clearly would be to admit that you're being a bit dishonest. But it's clearly present in the Gemara already -- הכא במאי עסקינן? That phrase and those like it are the sign that an illogical, contradictory, or otherwise problematic Mishna or Beraisa is being reinterpreted. Out of respect, the Gemara maintains the fiction that the Tanna'im meant something that they clearly did not. Subsequent posekim follow in their footsteps.
(This is why your essay on the kezayis was "disrespectful". Normally we take pains to pretend we don't think earlier posekim were wrong even if we're overruling them. You demonstrated at great length that they were wrong, without even the reason of needing to overrule them.)
Since each generation pretends to agree completely (not just almost completely) with all the earlier ones, someone who doesn't think about it much might be fooled into thinking the agreement is real. This isn't a bad thing -- it lends legitimacy to the religion. "We've always followed the same halacha" is much easier to teach and accept than "We generally follow the same halacha, except when particularly influential rabbonim change it." Most people will not cope well with sophisticated or subtle theology.
Anyone with much learning is not going to really be fooled, though. No one who knows anything can claim that the Amora'im would have agreed with all the halachos in the Shulchan Aruch. For the more sophisticated, we have principles like לא בשמים היא, and the story of the tannur shel Achnai and others in that vein. These emphasize that the accepted halacha is correct even if it's not exactly what earlier generations accepted.
But this isn't what's emphasized publicly, because it appears to undermine traditionalism. Talking about it undercuts respect for earlier generations.
As far as the gedolim not having the freedom to rule as they please -- this is inevitable until we once again have a central religious authority that can rule by fiat. The general population must choose whom to listen to somehow, if they're given a choice. It would make little sense to suggest that they should choose one posek according to their whim and then follow him forever no matter what, without ever considering a change to a different posek. Whatever guided their original choice can also guide subsequent choices.
Rabbonim always have to tailor their messages so that their flock will listen to them, whether that means supporting the political-religious ideology du jour, not mentioning halachos that their congregation doesn't want to hear about, or anything else. Rabbonim are not supposed to just mechanically produce halachos, they have to get people to follow them, and thereby follow Judaism. This will always involve political decisions.
I think nothing I've said here and nothing you've said in this blog post is specific to charedim or anti-rationalists. The only difference is perception and presentation. Modern and rationalist posekim overrule old decisions too, while also not claiming to be as great as the ones they're overruling. They're only somewhat more honest (i.e., less respectful) about what they do. The big difference is that they less often deny the validity of alternative positions, not that they have a different idea of how to arrive at halachic conclusions.
I would basically agree with everything that Aryeh said (except for his comments on my kezayis essay!). In fact, I have long studied and taught similar such ideas myself. Menachem Fisch, in "Rational Rabbis," argues that this is basically the purpose of the Gemara; to show how to change the rulings of previous eras without making it look as though that is what one is doing. Traditional societies are based on the idea of the authority of previous generations, and thus revolutions cannot be presented that way. Concepts like nishtaneh hateva are sometimes invoked even when those invoking them know full well that this is not the case, but by describing the situation in this way, they can change the halachah without undermining the authority of the earlier decisors.
Was not my previous post then seriously flawed in its focus? Was it not a criticism of the standard halachic process rather than a particular group of anti-rationalists?
It's true that the standard halachic process does involve quite a lot of this effective overruling of earlier authorities under the guise of doing no such thing. And this is something that is often bothersome to me, as much as I appreciate the necessity for it. And I do recognize that some of my writings undermine the values behind this process (I justify it on the grounds that people today are more knowledgeable and benefit from being filled in more). So, the basic approach that I criticized in the previous post is really a fundamental part of Judaism. Nevertheless, with the rationalist approach, it is significantly less troubling, for several reasons.
With the rationalist approach, it is understood that the authority of rabbinic decisors from previous eras is institutional. It does not stem from their being of superhuman intelligence or possessing divine inspiration, but rather from their unique historical situation and the consequent canonization of their rulings by those of subsequent eras. Since their authority is institutional, changing their rulings via halachic sleight-of-hand does not really undermine this authority. Furthermore, it is understood that any changes in halachah or theology do not reflect negatively on the earlier figures. People think differently in different times and places, and we are able to benefit from the advances of earlier generations, but we still respect the accomplishments of earlier figures and understand how they reached their conclusions even as we quietly diverge from them.
In contrast to this are the anti-rationalists, who will loudly insist that everyone acknowledge that the earlier generations were infinitely more intelligent and knowledgeable and holy, and yet toss their views out of the window and declare them a perversion of Judaism whenever it suits them. Deep down, they don't really respect the Rishonim at all; they just capitalize on certain mantras such as Rishonim k'Malachim in order to boost their own authority. Moreover, they attempt to suppress the right of others to still respect these earlier authorities and follow their approach, and they engage in large-scale revisionism of history in order to delegitimize those who follow the earlier approach. Now, I do understand their reasons for this - maintaining a certain way of life in face of the threats of modernity - but the aggression with which they impose this on others is jarring.
Furthermore, when there really are very good reasons to quietly diverge from earlier authorities - such as with organ donation - it is never done. Whereas in the past, this sort of divergence from earlier positions was done for pressing public benefit, today it only seems to be done in order to advance anti-rationalist agendas. The people ultimately wielding the power in determining the direction that these revolutions take appear to be the less-than-savory kanna'im and askanim rather than rabbinic leaders with wisdom and sensitivity to the needs of the generation.
It is true that the anti-rationalists are following a traditional approach of engineering revolutions that are deemed necessary (and I do appreciate the reasons why they see it as necessary) by effectively rewriting history. But the extreme nature of this revolution, in conjunction with the intolerance for those who really do want to follow the Rishonim for excellent reasons, the selectivity with which this approach is applied, and the nature of the people driving these revolutions, is what I personally find extremely disturbing.