It's funny that you use C99 as an analogy. Please list all the compilers you support that support C99. I'll give you a hint--MSVC, Clang, and gcc all don't support C99 fully, and possibly never intend to. It's not just an idle "oh, no one cares about those features; they support it for all intents and purposes": gcc kept its default standard at C89 in part because it didn't support C99 fully.
What you're doing when you say that you assume C99 compliance is you're thinking of the features from C99 that you want to use and relying on that. Admittedly, the generally-unsupported features are very niche. But that means that you potentially have a dozen different ideas of what "we support C99" actually means, and that's before you start asking how reliable an implementation needs to be before it meets the definition of "support." Declaring support for versioned standards is often more problematic than helpful (versioned implementations is a different story).
The real problem with autoconf is that no one removes the unnecessary feature checks and no one audits it to see what's still necessary for the platforms that people intend to support.
"C99 is substantially completely supported as of GCC 4.5 (with -std=c99 -pedantic-errors used; -fextended-identifiers also needed to enable extended identifiers before GCC 5), modulo bugs and floating-point issues (mainly but not entirely relating to optional C99 features from Annexes F and G)." [1]
Sounds fully supported to me, for all practical purposes.
What you're doing when you say that you assume C99 compliance is you're thinking of the features from C99 that you want to use and relying on that. Admittedly, the generally-unsupported features are very niche. But that means that you potentially have a dozen different ideas of what "we support C99" actually means, and that's before you start asking how reliable an implementation needs to be before it meets the definition of "support." Declaring support for versioned standards is often more problematic than helpful (versioned implementations is a different story).
The real problem with autoconf is that no one removes the unnecessary feature checks and no one audits it to see what's still necessary for the platforms that people intend to support.