Cmake and several other buildsystems either don't support cross-compilation at all (because their primary audience is Windows) or use pkg-config only. Few others are nightmarish parody of autotools with much worse support. Most don't have ounce of autotools features.
I know many projects, that offer horrible autotools "support": for example, glib2 autotools scripts can't be cross-compiled to Android without ample application of hacks. But those issues are caused by incompetence and lack of testing, not some innate fault of Autotools. When such projects migrate to something else, their cross-compilation process becomes WORSE.