[BUGFIX] LocalConfiguration cleanup breaks install process

The method to kick out obsolete settings from LocalConfiguration
in the install tool step installer is called too early and the file
may not exist already. Move the method call below step one of the
installation process that creates the file.

Change-Id: If3d824b6488c7cebfdef2a5b122aea9d47424983
Resolves: #49540
Related: #49299
Reviewed-on: https://review.typo3.org/21765
Reviewed-by: Wouter Wolters
Tested-by: Wouter Wolters
Reviewed-by: Anja Leichsenring
Tested-by: Anja Leichsenring
Reviewed-by: Christian Kuhn
Tested-by: Christian Kuhn