[BUGFIX] Fix no caching behavior of bootstrap

Install Tool and tests are intended to work
without caches being active.

Currently this functionality is broken in bootstrap
because it is applied too late and does not
respect classes cache.

Resolves: #56583
Releases: 6.2
Change-Id: I45bb11d3b7951b189c1f12c3da6969285575d72b
Reviewed-on: https://review.typo3.org/28088
Reviewed-by: Christian Kuhn
Tested-by: Christian Kuhn