Kind of? The spells are kept consistent, but that's hard-coded, so it'd be wrong if you found a way to skip the proper gates. The save file stores the current items and spells and stuff for both girls, but the same space is used by both groups. I could tack on more variables for the "other group's" items, and swap them at the appropriate times, but... it gets complicated. I'll look into it more seriously later, I guess.
Also, there used to be an oversight where 6-1 didn't reset items (so the moms had the girls' items), which let you bomb down to 6-2, which is iffy. If I were to add this, you'd be able to bring bombs there again via mom mode, so I think I'd have to do something about that. I don't doubt there are similar concerns elsewhere.