In my experience is it doesn't work. Sure it can be made to work and autotools asks all the right questions. However in the real world I have yet to see an autotools project that works out of the box in my custom environment.
Meanwhile cmake just worked every time when I plugged in the toolchain file that I created for the very first project I needed to build for my environment.
Again, it isn't that autotools cannot do what is claims. However nobody gets the details right and so something doesn't work. That something is different for every project. In the end what works is either what someone takes the time to make work and those things that are "very close". My project is cross compiling linux, which cmake does well (autotools also messed something up, often failing to use the sysroot paramater where needed)