[BUGFIX] adjust configuration handling to #55569

In #55569 we got rid of the empty TypoScript generated by
default. The configurationManager relies on the empty
arrays to be present, before merging. This patch removes
this necessity.

Resolves: #55687
Releases: 6.2
Change-Id: I7f5ec4f7d120ffa45c8b526817debbc5fd38fe4f
Reviewed-on: https://review.typo3.org/27350
Tested-by: Christian Weiske
Reviewed-by: Anja Leichsenring
Tested-by: Anja Leichsenring
Reviewed-by: Jigal van Hemert
Tested-by: Jigal van Hemert