pkgbase: set the prefix of debug files and macros to /usr/src

When the macro PACKAGE_BUILDING is set, then consider we are building package
for pkgbase, this has already been used in Makefile.inc1 and reuse the
PACKAGE_BUILDING macros already used for that purpose in the ports tree

In the future this should be tied to REPRODUCIBLE_BUILD

MFC After: 3 days
Reviewed by: emaste
Differential Revision: https://reviews.freebsd.org/D42569