I don't get this reasoning. You started off with a major overhaul without even experiencing what the mod changes in the first place?
How would you know what actually needed to be changed? How would you know that a change wasn't completely based on the authors personal tastes and actually might have made the game worse for you?
Simply by a lot of time in the forums. I read up on the game and saw one glaring issue players had in vanilla: no level scaling. I knew that I didn't want to have a level 25 character that had a hard time fighting a rat because the rat was level 26. And really, to be honest, I did start with vanilla for a few levels before I discovered the mods. When I saw all that was available, I stopped playing and did quite a collection of mods to start from scratch.
So, good catch...I don't remember in those first few levels whether I felt something was wrong and needed changing. I really don't think so. I think I found many threads about the level scaling issues and happened on the overhaul and was instantly intrigued.