Yocto builds entire packages twice, for build machine and target. It patches packages, doing whatever it takes. It makes use of QEMU also.

Sure, Autotools can do this and that ... given a significantly large and busy crew of downstream packagers who compensate for this and that in their distros.

It's a lame horse that needs to be buried.

The main thing that's wrong with Autotools perhaps is that it is shielded from fixes. Autotools makes a cockery of a project's configuration, and then downstreams concentrate on fixing the cockery to get that project working right. The fixes do not go back to Autotools!

There is already very little feedback between distros and upstream projects. Most of the time distros fix things silently, get things working and never contact upstream. (I've often learned of build issues in my projects by browsing downstream issues and discussions. They do not contact you! I would patch their problem. Then check a month later after a release and yup, "patch no longer applies; upstream fixed this; issue closed").

And now Autotools is one more hop behind upstream! Most people causing problems with Autotools will never be contacted, and those that are will never fix/improve or at least report anything in Autotools. If they do, they will probably just be told they are using Autotools wrong, go away.

Thus the Autotools project is blissfully oblivious to the idea that it might be a problem. Like an elephant in the room that is lying on your sofa, sipping a margarita and watching TV.