The capabilities may be there, but in my experience many if not most projects do not use those capabilities. Most autotools based projects I've had to cross build are made by people without a great understanding of autotools internals and capabilities, so they often end up copy pasting things blindly from other projects until they get their native build working. Advanced build system stuff like cross building is not even considered.
These builds end up trying to execute a binary to do feature tests, or compile a program and use that to generate code, or do any number of things that break when cross building.
Would things be worse without autotools? Maybe so. In my personal experience projects using a simple Makefile were much easier to cross build and package than ones using autotools, but that's probably confounded by projects using a Makefile being simpler overall.