At the end of the day, premade characters in a visual novel just make things easier, whereas a customisable character requires a lot of forward thinking.
But its also different styles of games which require different approaches.
Consider a game like "Long Live the Princess", whereby the protagonist is a faceless individual but who has clear interactions and relationships with other characters. They have a sister and an uncle, already defining how they should look and so makes the creator's job easier.
Now consider a game like TiTS, where by the definition of the game, the character will be changed at some point in the game. The writers and content creators have to account for at least some of those changes. For example, what if a character has two or more dicks? Do you put in a section of a scene to account for that? What if they're Tauric or a mass of tentacles? Now imagine someone trying to account for that in a 3D environment and watch their head explode. It works in TiTS because instead of trying to render everything, you can write it and build from there.
A premade character has its own advantages and disadvantages and likewise, a customisable one will have their own. If you just have a story to tell, then the premade character allows you to focus on the story, even if you risk alienating some of the readers, whereas if you want the focus of the game to be people creating their "ideal" self, then you can focus on that aspect through text.