Since the normal way of telling your operating system where to look for libraries is (on Linux, mind you) to modify /etc/ld.so.conf and friends (like included files in /etc/ld.so.conf.d) and since pkgconfig will look in /lib hierarchies like /usr/lib/pkgconfig, I believe that the correct behaviour of pkgconfig would be to try to retrieve library locations from /etc/ld.so.conf (+friends) and try to append "pkgconfig" after these paths so as to locate libraries in exotic places. Currently, if you put a library in /usr/local/lib par example, and then the .pc file goes into /usr/local/lib/pkgconfig, then modifying the /etc/ld.so.conf file does not help pkgconfig to find the .pc file. IMO it should.
/etc/ld.so.conf is only used by the runtime linker (ld-linux.so), not by ld and gcc. I don't think having pkg-config care about the runtime paths makes sense. However, pkg-config is going to grow a feature where you can specify a list of directories to look for .pc files, so you should be able to specify the search path when building.
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