pkg-config: rework --with-sysroot patch so it doesn't break target build

We don't currently autoreconf pkg-config for the target as we don't need
--with-sysroot support, which means PKG_CONFIG_SYSROOT=NULL wasn't
passed, breaking the build.

Fix it by reworking the patch to only pass this if --with-sysroot is given,
and handle the not set case in main.c.

Signed-off-by: Peter Korsgaard <jacmet@sunsite.dk>