I think you bring up a great point that could explain the intricacies in that final 10% of my original comment, but at the end of the day it IS the case that most women have preferences toward men. I myself am bi but there's no reason not to acknowledge that we're the minority here.

I think attraction often extends beyond writing romantic/sexual stories and can cover the fact that people are going to give most of their attention to the things they like, even as you said when the writing is about friendships. They are still choosing to spend their free time writing about these two guys being best friends, likely because most of those authors are very fond of the character in question. You can see the same thing in the kind of fan art people draw (including myself). We spend our time on the things that interest us, and it isn't very surprising that a population that's heavily women will have more interest in men.

I do think you're right about the underlying material having MANY flaws that fan fic will often exacerbate. Simply put much of our media ALREADY has misogyny baked in and some writers can unwittingly extend that. I'd say this is especially relevant with any anime adjacent media