Still catering for pre-C89 compilers in 2003 was questionable. Doing it 20 years later in 2023 is beyond questionable. It's not a portability problem any one of us has had to care about in decades. And it's now a source of problems because it's breaking with current tools. That defect is squarely upon them.
Portability problems are of their time, and old workarounds can be dropped once they are no longer required. Many of the Autotools checks and workarounds are for platforms which were retired decades ago. The whole lot could be deleted. When you look at the cost:benefit of them, they are utterly niche and are largely untested by anyone. When you actually look at which tools are portable in practice, the autotools are usually worse than the alternatives like CMake, because they ceased to keep up-to-date with contemporary systems.
As the other poster mentioned, the fact that the generated code is embedded in thousands of projects, all of which need independently updating is another aspect of its design which should also have been retired once the tools reached maturity. There is zero need for this, just require them to be installed like any other build dependency.
The issue here is that functions are called without a function prototype, aka the proper headers included. The compiler basically guesses what the function prototype is. This is certainly error-prone, and the fact that autoconf relies on tons of test code pieces that aren't really correct C code is if anything worrying.
It's also probably a good thing that this shows up first in clang, as most linux distros are built with gcc, so you have a testbed to fix all that stuff. gcc should eventually catch up and introduce the same default.
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