Here, Rashba argues that it is impossible to claim that only phenomena for there is a rational explanation are real and permitted. His reason is that there are phenomena that undeniably exist, and yet for which there can be no scientific explanation. The example that he brings is the magnet, and its use in a compass. These things operate neither in the realm of the miraculous, nor in the realm of the natural; instead, they operate in the realm of segulah. Rashba notes that "the wisest of scholars in the sciences can never grasp the nature" of such things.
Now, I myself, in my monograph on demons, argued that one cannot simply assert that those who believed in demons and suchlike were not rationalists. Things looked different in the medieval period, and some people believed in such things for rational reasons. Nevertheless, there is still an enormous gulf separating the rationalist Rishonim of Spain from the mystical Rishonim and from the non-rationalist Rishonim in Ashkenaz.
Superficially, Rashba's discussion appears not too far removed from that of Ralbag. Ralbag was an extreme rationalist, yet he likewise asserts that magnets can only be explained in terms of being a segulah. However, the term segulah as used by Ralbag (and Rashba) has been borrowed from pharmacology, where it refers to peculiar properties which cannot be explained in terms of its constituent elements (see Y. Tzvi Langermann, "Gersonides on the Magnet and the Heat of the Sun"). In applying it to magnets, Ralbag is claiming that the nature of the magnet cannot be grasped by the science of his day; but he is not explaining it to be a supernatural phenomenon, and he did not see it as reason to accept the validity of magic.
For Rashba, on the other hand, there is no distinction between that which science cannot currently explain, and that which it will never explain. Rashba's point is not that there are "empirically tested phenomena work through the principles of science despite the fact that we do not understand these principles." On the contrary; his view is that there are principles other than laws of science and nature that operate. Unlike Rambam, who realized that magnets are a solely naturalistic phenomenon, Rashba believed that magnets operate in a different realm - that of segulah. According to Rashba, the framework within which segulos work is precisely not the framework of science and nature. He therefore sees magnets as reason to accept belief in magic and all such phenomena. The lack of any conceivable scientific explanation for a phenomenon is no reason whatsoever to doubt its existence.
Now, it is true that even today, we don't really understand what magnetism, or gravity for that matter, actually is. We can measure and describe how it works, but we still don't know what it fundamentally is. Nevertheless, we are fully confident that it is a natural, rather than supernatural, phenomenon. Rambam and even Ralbag felt the same way, which is why their inability to comprehend magnetism or other phenomena did not prevent them from dismissing other phenomena as clearly false. The line between science and pseudo-science is not always clear, but there are nevertheless many things that we confidently dismiss as non-existent. Rashba, on the other hand, did not believe that we can ever dismiss phenomena as scientifically impossible and false - and saw magnets as evidence for this.
It's nice, and very tempting, to think that whatever we believe to be the correct approach to Judaism has always been the approach of great Torah scholars. However, that is often not the case.