There are advantages and disadvantages of every gaming engine. Ren'Py doesn't really work for a game in WASD style, for instance, whereas UE is built to handle that. There are out-of-the-box features in Ren'Py that can be implemented in other engines (rollback, history, show/hide UI, etc.) fairly easily, depending on the engine.
One of the big advantages of Ren'Py is as you say: you can mod and adjust it fairly easily. However, I wouldn't say it's "silly" to dislike the idea of creating a story and having someone come along and completely change things. Suddenly your story no longer resembles what you wanted to tell. What seems "silly" to me is everybody and their dog feeling the need to reject what a creator has made and do their own take on it.
Small mods (like adding incest) generally are fine, but forcing something like a harem when it was never intended are excessive and almost never work well. The dialogues and events start feeling very forced and of poor quality. If you want a different story so badly, just create your own game. I wouldn't avoid using Ren'Py just because people tend to want to manipulate the hell out of what developers have made. However, TBH I do find the perspective a little offensive that an author's vision is practically worthless — what it effectively amounts to when you say it's "silly" to be worried about others changing their story.
