You don't think there is any degradation in your ability to deal with source code if you have no idea that it's got various patches and where they come from? If your copy includes patches and a process to install them, it's a matter of a few minutes to compile without one of them (if it has no dependencies) because you don't want it. With a big ball of source code, you'd have to track down the original patch and see about how to reverse it - much more complicated.

It's clearly not impossible to change the program, but you have lost information. I don't think it's "obfuscation" in the traditional sense, but it's certainly not what I'd call friendly, either.