Turns out Kaphotics fixed all of the Gen I issues (that I was seeing at least) in a dev version around the time I made this post: https://github.com/kwsch/PKHeX/issues/2964#issuecomment-673888005
You can either download said version (linked in the comment I linked to) and build it (I used Visual Studio 2019) on your own, or you can simply wait for the next official version of PKHeX which should have these changes.