For a project like KDE, the amount of changes needed in the KDE code itself to port to a platform like AIX dwarfs the amount of code changes needed to make CMake run on that platform. So if it makes work easier on the common platforms, it is a better deal, and ports can still be done by porting CMake first.
As for autotools I have never seen them be that useful in porting. Sure, autotools may run on all sorts of systems but nothing out there tells you what autotools tests and variables your code needs to be checking for portability.
For example, assuming select() returns the remaining time from a timeout. If you develop on Linux and rely on that feature, then port to another Unix, autotools may have a test to detect that for you but you have to try the port and find the problem first before you even know you need it.
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