Clarify autogen.sh messages

Actually warn the user, if we ignore provided configuration files.

Also add an extended header to explain the expected behaviour.

Change-Id: I630d858c2d24aa0341d04359b45029c7faa54675
Reviewed-on: https://gerrit.libreoffice.org/8446
Reviewed-by: Norbert Thiebaud <nthiebaud@gmail.com>
Tested-by: Norbert Thiebaud <nthiebaud@gmail.com>