It could. But it's an incredible coincidence that it's always cmake projects.
Generally on nonstandard installs the others (e.g. scons) won't even run, so portability of the conf is not relevant.
what are you talking about ? take for instance kcachegrind, it builds with cmake and works on every architecture that debian supports (https://packages.debian.org/en/sid/devel/kcachegrind). I also never had issues with x32 when I used it, nor on freebsd. Can't say for openbsd but I'd be surprised it does not work there - this seems to point that other than a minor path issue things just work: https://www.sizeofvoid.org/posts/2020-03-29-how-to-build-qt5....
I'm not saying CMake itself doesn't work. Though I have run into both "CMake version is too old!" and "CMake version is too new!", which by its nature can't happen with autotools.
The reason it hasn't been seen recently is that there has been no significant development of note for the past 15 years.
Even so, it's still common for the distributed config.sub and config.guess to be outdated. That's the price you pay for embedding stuff in each package, as opposed to requiring the build tool to be provided on the build system just like all the other tools.