but if I need to create changes for app2 in core, should I then create a :core-core, with base class, and then :core-app2 with the mutation? same for app1 now

You act the same as if you have similar features inside the same app: you abstract out the common behaviour and use inheritance/composition to implement the differences

You can have different flavors and have different implementations of the same class under the flavor folders

Yes @Anastasia Finogenova is right, flavor seems to be a better way if you are at 90% shared code. If your 2 apps do the same but with differents "wrapper" (colors/app name/icon/premium function), flavor fits very well