CMake is doing more than generating a build file, it's also a configuration tool (detecting compiler, finding dependencies, etc).
In general though, if you're just talking about small projects, I have found the easiest way to incorporate smaller librares into a build system is to just ignore whatever build system they are using and re-write the build in the larger build system (even if they are the same tool!). This is mostly because the current state of build systems is so terrible.
What you say is true, but it can be interpreted as either positive or negative features. I would say that code that depends on specific versions of a library or specific compiler options is bad code; and propagating bad code instead of fixing it is not a good idea. Cmake makes it very easy and convenient to ship bad code, as you explain. Thus, it is a force of evil! It allows, even encourages, the programmers to be sloppy without short-term visible consequences.