Hey! I am just curious, is your molly, a dalmatian molly? The only reason why I ask is that I have a dalmatian molly that was in a similar situation as yours! Her name is Bea and she started off as all black, however, over the months she ended up showing her true colors and grew into them and she ended up being like an oreo-themed fish. I am just curious to know if the isolation in your molly's tank has prompted new conditions to improve and further provide an environment where your molly can grow.
Based on the pictures, it seems that it is based more on the skin of the molly itself and does not look to be fungal (in my opinion! I have seen ich time and time again and to me, that does not look like ich, it looks more like a change in scale color rather than anything else).