Well it makes sense sometimes to do that and sometimes it doesn't.Giving the player options like this, in a vn engine is practically unheard of so this dev deserves an honorable mention for his undertaking. There are a lot of games out there that I might like, if the girl wasn't a blonde.
I highly recommend rendering characters separate form backgrounds. This helps keep the game file download size from becoming unmanageable.
In this situation, I would render the base body for each character, and 3 pairs of disembodied boobs, and 3 hair colors simultaneously (for lighting purposes) then crop the boobs and hairs into png overlays
layer the png in game... background, midground, character, options, foreground.
This means 1 render, rather than nRenders per option.
1) jpg images are a lot smaller than png
2) shadows and interactions of characters with background can make it impossible to render it separately. At least not in good quality. You want see any floating in the air stuff in this game.
3) rendering parts of a body separately is not practical and also impossible without loss of quality.