[TASK] Have SilentConfigurationUpgradeServiceTest functionals

Turns existing unit tests into functionals, making
them more concise, avoids mocking parties, and
makes them better maintainable.

SilentConfigurationUpgradeService is slightly
cleaned up along the way, together with a minor
fix regarding a missing BE/lang/debug removal,
which was now found by the functional tests.

Resolves: #100407
Related: #100249
Releases: main
Change-Id: I9188af068243b3beacc56ab7c9a24f6536c46ed2
Reviewed-on: https://review.typo3.org/c/Packages/TYPO3.CMS/+/78377


Tested-by: Benni Mack <benni@typo3.org>
Tested-by: core-ci <typo3@b13.com>
Reviewed-by: Christian Kuhn <lolli@schwarzbu.ch>
Tested-by: Andreas Fernandez <a.fernandez@scripting-base.de>
Tested-by: Christian Kuhn <lolli@schwarzbu.ch>
Reviewed-by: Benni Mack <benni@typo3.org>
Reviewed-by: Andreas Fernandez <a.fernandez@scripting-base.de>