Fixed, although somewhat unrelated:
https://github.com/kwsch/PKHeX/commit/14821dfb82ad6015417823f2491a0477535973e1
PKHeX gets the base species then enumerates the chain to see if any of the catch rates match. You'll have to temporarily set it as the original species from another unrelated chain:
Pigeot -> Mewtwo -> Pidgey -> Pigeot
0 -> 3 -> FF -> FF
I don't think it's a big enough need to have direct editing of the catch rate; may necessitate a new custom control (Auto checkbox, species selection, raw entry) which is a bit of effort for something so minor.