We use a similar trick to libvirt to allow external C programs that
use libguestfs to be compiled against the built (but not installed)
libguestfs with:
../libguestfs/run ./configure
make
What actually happens is we have a second pkg-config file
(lib/local/libguestfs.pc) which points to the locally built
libguestfs. The ./run script sets up PKG_CONFIG_PATH to point to this
directory. Assuming that ./configure is using pkg-config/pkgconf and
not some other half-baked solution it will pick up the libguestfs.pc
file from here which will set CFLAGS and LIBS appropriately.