That would only work for projects that care only about current compilers, where C in general has more desire to support niche compilers.
A mitigation here would be to make result of autoconf only provide instructions for humans to change their build config, instead of doing it for them silently. The latter is an anti-pattern.
FWIW, the approach you propose is how the UI tests for rustc work, with checks for specific annotations on specific lines, but those have the benefit of being tied to a single implementation/version and modified in tandem with the app. Unless all compilers could be made to provide reasonable machine readable output for errors, doing that for this use case isn't workable.