fragments: handle sysroot dir munging directly in a smarter way

Previously we just let the tuple system handle it, but pkg-config modules which do not define
variables were able to get by the checks.  While here, check to ensure we do not duplicate the
sysroot dir twice if it is already defined in the pkg-config module file.

Downstream bug: https://bugs.busybox.net/show_bug.cgi?id=5750