Problem is I do tamper with those. I often cross compile software (my day job is embedded linux). Different distributions like to put things in different locations for their own reasons. I have a multi-core computer and I'd like to use more than one of them so my build goes faster.

As a developer I don't want to have to worry about how to make all of the above work. I learned cmake and so I don't have to worry, now that I know it (the learning curve is there) almost all my issues go away because it just works with all the weird stuff people do.