python3: Remove problematic paths from sysroot files

In the native sysroot we should never have paths to the python3-native
build directory. These may or may not exist at the time some dependency
is building and nothing should rely upon them.

I suspect nothing is relying on this at the moment but clean up
just to be sure.

The various config copies are adjusted to be modified consistently as some
copies were and some were not. The Makefile has the "bad" ${B} paths
replaced with a dummy placeholder too.

Signed-off-by: Richard Purdie <richard.purdie@linuxfoundation.org>