If we were to split the leaderboards, I like the idea of splitting it AMD+FPSFix / other. It gives AMD users who want to compete and compare with Intel users an option to do it. At the same time, AMD users who need to use the Fix in order to be able to play the game smoothly or want to use it for other reasons would have a leaderboard to submit their runs to.

Another issue stemming from it is if we'd allow AMD users on the "other" leaderboard to use OneTweakNG. FPSFix is a fork of OneTweakNG that additionally removes the frame pacer and offers some graphical fixes. The removal of frame pacer seems to be the main reason why FPSFix improves the framerate. OneTweakNG alone also makes the game run a bit better (at least for me), while not offering the "speedup" that FPSFix does due to frame pacer removal.
Thus, I don't see any drawbacks of allowing AMD users to submit runs with OneTweakNG to the "other" leaderboard if they wanted to compete with Intel users while still having some sort of fps improvement. If anything, this would put them at a disadvantage compared to Intel+FPSFix users.

It should be also pointed out that whatever we decide would probably have to be propagated to the longer categories' leaderboards. And then there's the very niche issue of Trilogy% leaderboard, if more AMD+FPSFix users would want to run that (and I know Pharaoh showed interest).

Overall, I prefer splitting the leaderboard in some way over banning the Fix completely, as it does allow a lot of people to fairly comfortably run the game, which would otherwise be basically impossible. Even if that's how it often is with PC speedrunning.