Autotools is rarely portable. I've been doing a lot of cross compiling recently: the vast majority of autotools projects can't be cross compiled. Sure autotools itself supports it, but something required to make it work didn't get connected up and so you can't do it.
If you want to natively compile on a fairly recent linux with the common standard libraries autotools works well. Even though autotools was written to work around these differences, in most cases the developer didn't hook into autotools detecting that difference and so it doesn't work.
Embedded Linux on arm. Nothing very far out really. Note that I'm careful not to blame autotools, it is the user's fault, there are a couple projects that use autotools and cross compile easily. The vast majority do not.
CMake based projects almost always cross compile easily.
If you want to natively compile on a fairly recent linux with the common standard libraries autotools works well. Even though autotools was written to work around these differences, in most cases the developer didn't hook into autotools detecting that difference and so it doesn't work.