[TASK] Add note about AdditionalConfiguration.php to Install Tool

Add a note to clarify that AdditionalConfiguration.php is always
overruling any setting made within the Install Tool.

Furthermore we add a note to the ConfigurationManager that it is limited
to Core internal usage only.

Resolves: #60650
Releases: master, 6.2
Change-Id: Icaf7d4b1ce5b14ad0618e38e92a49a33405997f7
Reviewed-on: http://review.typo3.org/35412
Reviewed-by: Anja Leichsenring <aleichsenring@ab-softlab.de>
Tested-by: Anja Leichsenring <aleichsenring@ab-softlab.de>