I do not understand what you are getting at.
You use a high level programming language. You use an ide. You use libraries that someone else made. Do not belittle people doing the same. It does not lessen a game.
Using a game engine is literally using a high level programming language and using the specialiced libraries and framework that the engine provides.
Bitching about wich programming language is best, is nothing new. But you act, like it lessens or enhances the game made with it.
Also, you should not forget the topic. This is about vn. That reads visual novel, in case you forgot.
What do you think is more important when making a vn: the writing of the story or the programming of displaying pictures and sound and reacting to user input?
Of course it is usefull to be able to code on lower level, but as I said, in most engines you can include your custom made code if desired or even needed. Because of that, one should carefully decide the engine to be used. For some projects a self made engine might even be best, especially if it is easy tasks and you already know how to programm. But get used to reinvent the wheel a lot and have common pitfalls and mistakes and flaws, like fullscreen issues, corrupt save games and a plethora of other tiny details you did not think about before starting to code. All those things are pre-solved by a good engine, so you can concentrate on the needed writing and logic for telling the story. And maybe even doing some Art, instead of using premade assetts.