Why do some tools have this problem, and others not?
I think it's convention over configuration. Makefile can do anything, so every project is different and needs different configurations, and everything must be configured. Which means that when I use a tool like that, it's sooo many decisions to make, that I just copy something that I know works.
If instead it was some sane defaults, it would be pretty apparent where it deviates. And instead of thinking of hundred things and which to choose, I either don't think about them, or think "do I have a reason to configure this instead of using defaults?"