[BUGFIX] Failures in em unit tests due to phpunit update

Young phpunit versions seem to handle clones a bit differently,
resulting in test failures in extension manager tests. The tests
are adapted a bit to fix this.

Change-Id: If70561743f68a62167e41ee4c23ae96b56f83ab9
Resolves: #50478
Releases: 6.2, 6.1, 6.0
Reviewed-on: https://review.typo3.org/22604
Reviewed-by: Wouter Wolters
Tested-by: Wouter Wolters
Reviewed-by: Anja Leichsenring
Tested-by: Anja Leichsenring