Cross compilation for distributions is a mess, but it is because of a wide proliferation of build systems, not because of the GNU autotools -- which have probably the most sane way of doing cross compilation out there. E.g., distribution have to figure out why ./configure is not supporting --host cause someone decided on writing their own thing ...
> The main idea behind Autoconf is political. Autoconf based programs are deliberately intended to hinder those who are able to build a program on a non-GNU system and then want to make contributions while just staying on that system, not getting a whole GNU environment.
Nothing could be further from the truth, GNU autoconf started as a bunch of shared ./configure scripts so that programs COULD build on non-GNU system. It is also why GNU autoconf and GNU automake go such far lengths in supporting cross compilation to the point where you can build a compiler that targets one system, runs on another, and was build on a third (Canadian cross compile).