I want to run sonic Gens completely legit but I have a physics mod for shadow gens enabled because his gameplay is slower than i'm used to. but would enabling that mod also make sonic faster in game? therefore making all the runs I submit invalid?

We don´t have a answer to that, because we´re not modders of this game. In theory it shouldn´t since Sonic & Shadow Generations are 2 completely different games. Just to be on the safe side we recommend turning everything off. Mods will not be allowed for now.

Thanks!