I mean, autoconf is basically a set of template programs for snffing out whether a system has X symbol available to the linker. Any replacement for it would end up morphing into it over time.
We have much better tools now and much simpler support matrices, though. When this stuff was created, you had more processor architectures, compilers, operating systems, etc. and they were all much worse in terms of features and compatibility. Any C codebase in the 90s was half #ifdef blocks with comments like “DGUX lies about supporting X” or “SCO implemented Y but without option Z so we use Q instead”.
Some things are just that complex.