What you don't understand (and what I thought was clear in my post, but apparently wasn't judging by the flavor of most of the comments) is that bootstrap is not a baseline. You don't start with bootstrap and then build out custom code on top of it. You either use bootstrap or you don't use bootstrap. There's no skinning bootstrap - it is the skin. You don't start with it then change it to fit your design, you start with it, and then you are stuck and end with it.
This point that you didn't get was the entire reason behind why I made this post, and was the reason for the paragraph at the end, where I said that I was working on a different type of framework that you can start with then pull apart in a modular way as your product moves forward without losing the ability to write your own code or having to hack away at a core codebase.