> [...] treated some of the code used for various feature checks invalid and the end result was checks failing even though they should have passed - often with barely any notification to the user (the user would see a "no" instead of a "yes" in some check)

This is a perfect illustration of conceptual bankruptcy of the autoconf approach. Using compile/link tests and basing a decision on whether they succeeded or failed without distinguishing the reasons for failure will inevitably lead to silent false negatives.

If you are wondering what to do and what are the alternatives, here is one approach: https://github.com/build2/libbuild2-autoconf