I kinda want to customize the protagonist fully like say I wanted to make a green hedgehog or a tiger print tuxedo cat but I know that's a bit too innovative for a visual novel
Hah, not really! Coding wise, it'd be very easy to implement. The issue is the art, aka: for each variation you'd need to commission a different sprite. Some things can be re-coloured procedurally in the engine, but not everything.