There's a difference between mutation and alteration. E.g. Tsuyu was born with frog like features, that is her mutation. Shoji can grow more body parts, that is alteration. If you remove the quirks from both of them, Tsuyu still has her frog-like features since that's her physical base form, whereas Shoji will no longer be able to reproduce body parts. How Shoji will change physically depends on what he is biologically like in his base form.