[CLEANUP] Clean up configuration handling in module loader

* Merge label configuration like module configuration
* Correct the merging to be replace instead of merge
* Remove possible notices by checking with empty()

Releases: master
Resolves: #63717
Change-Id: I325e2f35cfe643a54e7f77a76cd8ce2901b950b6
Reviewed-on: http://review.typo3.org/35208
Reviewed-by: Wouter Wolters <typo3@wouterwolters.nl>
Tested-by: Wouter Wolters <typo3@wouterwolters.nl>
Reviewed-by: Markus Klein <klein.t3@reelworx.at>
Tested-by: Markus Klein <klein.t3@reelworx.at>