However, I think you trying to solve a non-issue, I'm not trying to solve anything. I'm trying to suggest CFLAGS's meaning should be documented in a place where maintainers might look during development. I don't see how it hurts to add a sentence or two.
I.e., he will typically add some *_*FLAGS macros/AS_SUBST's and use them inside of his hand-crafted Makefile.in's. The whole reason I wrote is because I found that in one package (grep), someone had added code to the configure.ac which added options to CFLAGS (specifically, the result of `pcre-config --cflags`), obviously because they did not know CFLAGS is intended for the user. The current Autoconf documentation gives a misleading impression about that. The programmer's mistake is completely understandable, of course, since outside of GNU (and autotools), it is common to use CFLAGS for necessary compilation options. All we can do is try to document it as best we can. Hence my message.