Autotools was always horrible, but it had a purpose back in the 90s, since then it's entirely vestigial and does nothing useful. It standardizes flags to config scripts and make targets, yes, but you can follow that standard without actually using autotools. It enables cross-compilation, yes, but the far biggest roadblock to successful cross-compilation is autotools, without that it's pretty easy.
Meanwhile, these days, actually trying to build on a new platform is harder if the software is using autotools than if it's using plain makefiles. Because for all the noise about feature checking, nobody including the projects using autotools, are actually using the defines from autotools, they check the OS or architecture.
I currently make my living porting software to non-Linux and non-x86_64 cross-built systems, and I can vouch with certainty from lived experience that your assertions are entirely untrue.
Meanwhile, these days, actually trying to build on a new platform is harder if the software is using autotools than if it's using plain makefiles. Because for all the noise about feature checking, nobody including the projects using autotools, are actually using the defines from autotools, they check the OS or architecture.