If I change the 45 catch rate, though, wouldn't that make it illegal in Gen 1 at least? I'm not sure why PKHeX mentions Gen 2 if I pick the Gen 1 games anyway (I assume since they can trade together, but eh). Since it's definitely a 45 catch rate regardless.
Regarding the Mega Drain part, I manually put that there with PKHeX since it was highlighted green. I thought the green meant it was fine to put onto Kabuto and stay legal. Would it be hard to code something within PKHeX so that for Gen 1 games, it only lists Gen 1 moves it can actually have from Gen 1 itself (and the other Gens that do this)? The catch rate is 45 is Gens 1 and 2 either way, though, so I'm still confused on changing the rate if it's 45 in either Gen1/2 games.
Basically, I'm confused since even if it's a Kabuto in Gen 2 and you did give it a a Bitter Berry or whatever, at the end of the day, the catch rate is still 45 in Gen 2 so I don't know why having it as 45 in Gen 1 (how it legally is obtained anyway) makes the error happen. Know what I mean? Sorry if I'm explaining this poorly, just woke up. How do legally-obtained Gen 1 Kabuto get traded to Gen 2 then on the cartridges anyway? Still 45.
EDIT: Just found this reply by you touching on the same topic and I noticed you said, "Catch Rates are modified when transferred to Gen2," but in this case, Kabuto's catch rate is 45 in both Gens?
https://projectpokemon.org/home/forums/topic/57375-pkhex-new-update-legality-errors-contribution-page/?do=findComment&comment=269388
I'm thinking the optimal thing to do would get rid of the green highlighted moves if that particular move can't be learned in the Gen it is from or something.