" it'd have to be done for all of them " - but why? A shield could be drawn behind the character, why sword - on top. Same for armor. So, if it's in accurate layers, it doesn't have to be tons of different variations.
" If we reach the point where I can implement ..." - yeah, I agree, it's a good idea to add things and stats slowly when needed, not over complicating things. Though it would be fun to see some changes or statistics, depending on your sexual scene choices. Like, some people can try to only fight with monster and have fun with only pretty human girls, but use items and events that will increase their corruption, while others will try not to fight, but fuck with monsters, which will, probably, also rise their corruption. So, at the end both type of players will get same looking/acting hero? Maybe there should be at least some sluttiness/dom/sub meter to make a difference? But, I agree, you can do it at any point when needed.
" As for questions of customization..." - agree. If it's more like a visual novel than text game, there is not much for visual customization. But, just in case, some advice here (have an experience) - ask your artists to paint in layers and give them to you. Everything. As many layers, as possible, each object. It will simplify future editing, when needed, and you'll not have to have 27 images, that would come from 3 background variations, 3 character1 and 3 character2 variations.