I know modern batman and arkham joker do count but will bombshell catwoman for example count for the catwoman matchups
I hear people often complaining about how their Bombshells don't count at all, so I haven't really tried with any other skins rather than the original ones. :/
In theory, yes, they should all work since it's still the same character overall just with a different outfit. However, there have been times in the past where certain Legends with variant skins didn't count properly towards certain team-up Feats due to either a bug, or a simple oversight while it was on Test that then went and made it on to the Live servers. Either way though, this would usually just get Hotfixed within a week or so and people could then get the Feat(s) they needed.
Bombshell supergirl definitely does NOT count in smallville. Have tried many times. Tickets have been created but no change yet.