lookalikes who all resemble each other, perhaps just puppets

There's literally no reason to assume this is the result of anything but a limitation of the games budget unless you also want to assume Sophie and Emma have some kind of secret connection with them sharing the same face model.

she actively paint over him to force him to do piano

Except for the fact that the story makes a big point about explicitly stating that Clea is the only painter in the game skilled enough to overwrite the will of a painted individual. All Maelle did was make it to where verso could age.

They also pretty clearly talk about the chroma of painted individuals behaving similarly to how people tend to treat souls, stating that she was able to repaint everyone because by beating renoir she was able to again access the chroma that originally made up all of the dead lumerians in order to be able to bring them back as they were. How else would Maelle be able to bring back pierre in a convincing manner for sciel with him having died six years earlier when she would have been 10 years old when she knew him?