The visible/invisible MC sprite is the very first I've ever seen...and it's such a great idea, how come I've never thought of that before??
Not that I'm any game dev, it's just I have seen so many VN's with no MC sprite for easy variance and customizability, but also losing a visible figure to present the MC...and the ones with one or two sprites to choose from but lacking character customization. (I personally wouldn't object to a given sprite, but surely there are many people who prefer otherwise.) A combined method is like a solution for both sides.
(PS: haven't played much of the game yet, but I just can't help commenting on this particular part XD)