Sorry, I don't see a bug there. "gcc -std=gnu99" accepts ISO C11, in the sense that it passes all the C11 tests that we have, if your version of GCC is sufficiently new. This is because the GCC supports these C11 features even when running in C99 mode.
If there's some C11 feature that is missing, a feature that it's reasonable to expect from C11 compilers, we could add that to the test, and this will cause 'configure' to say "no" rather than "yes". I did briefly try to think of such a feature but came up dry.
