>>34518378A child lacking individuality from a parent when they are younger isn't that weird. Lillie continuing to have her outfits chosen by her mother makes sense with how coddling she could be. It doesn't sound like Lusamine was forceful about the outfits in the game, Lillie just didn't know anything else because of her secluded life. Lillie's escape with Nebby was pretty much her finally putting her foot down and establishing individuality and discovering the world for herself.
The way things are in the manga implies Lillie was already her own person making her own decisions and Lusamine tore that all down. This is significantly more sinister on Lusamine's part. Specially if she has Lillie so scared she's still wearing the outfit despite all that.