Joseph: And how do we know a lot of things? At some point you have to trust that there is Siyata Dishmaya in our knowledge. How do we know our Girsaos in the Gemaros and Rishonim are right? Some of the Geonim had radically different Girsaos in entire Sugyos. And don’t get me started on Girsaos in Kodshim, especially M’ilah.
The fact is, HKBH doesn’t expect us to get these things right. He expects us to do our due diligence (which doesn’t necessarily include historical research) and try to learn the best we can and the rest is just Siyata Dishmaya. In an issue on which I am confident that there is overwhelming historical evidence that a Minhag is a Minhag Shtus, we can assume that HKBH wants us to recognize that it’s a Minhag Shtus.
A parallel case: I have a distant relative who removed/covered all mirrors in the house when she had her first child because if an infant sees their own reflection before their teeth grow in, their teeth will never grow in. In fact, I could find you a source in a relatively-recent Sefer that says such a thing. Now, empirical evidence dictates that babies see their reflection in the mirror and yet their teeth still grow in. We can research how such a Minhag/superstition came about (it is not limited to Judaism in the slightest), but the empirical evidence saying the reason is false, coupled with the fact that I can find this superstition mentioned in secular sources long before it’s ever mentioned in a Jewish source, tells me it’s a Minhag Shtus and the Sefer that quoted it was just relating what he had heard from superstitious people on this and made the same “Im Lav Neviim” assumption.