infra: /usr support: STAGING_DIR can be outside BASE_DIR

If the user sets a custom BR2_HOST_DIR, then STAGING_DIR is not under
BASE_DIR. The .pc/.la file fixup commands incorrectly made this assumption
and thus should be corrected.

Additionally, this patch:
- rewords the comment in pkg-autotools that explains the replacements.
- removes a for statement in favor of xargs

Signed-off-by: Thomas De Schampheleire <thomas.de.schampheleire@gmail.com>
Signed-off-by: Peter Korsgaard <peter@korsgaard.com>