I think you mean Unix, not GNU/Linux. Porting from one flavor of Unix to another is the raison d'etre of autoconf. It's really quite valuable when you're the one in charge of babysitting 20-year-old AIX or HPUX boxes.
It's not even meaningful to talk about using the autotools on a non-Unix platform, since autoconf emits shell scripts. It sounds like you've run into problems with automake on a non-Unix platform generating Makefiles with shell code in it?