While I do agree this being an AIX bug, it is not a blocker here:
fcntl extension does not _depend_ on flock, it just does _prefer_ flock:
If not available, fcntl extension uses something else (fcntl IIRC), as it did (even without linking libbsd) before the AIX5.3-patch, which just added flock to the headers (the implementation in libbsd already has been there before the patch).
The problem after that AIX5.3-patch was that the compile-check found flock, and then fcntl extension failed to link due to missing libbsd.
So it's just for how to detect flock, where the most safe variant is both the compile- and link-check. When one of them fails, flock should not be flagged as available and the alternative gets used.