[BUGFIX] Prevent repopulating TYPO3_CONF_VARS

Instead of using the native API when changing a TYPO3 Extension
configuration through the new ExtensionConfiguration API, the
method is now solely overwriting the global $TYPO3_CONF_VARS[EXTENSIONS]
and $TYPO3_CONF_VARS[EXT][extConf] options during runtime
to avoid deadlocks and to avoid the removal of existing configuration
of extensions.

The second parameter of ExtensionConfiguration->set() can be removed
separately once EXT:bootstrap_package is adapted to the new functionaliy.

Resolves: #83958
Resolves: #83954
Releases: master
Change-Id: Icc8a3482edaef1ea329e68638d5ef467548062fc
Reviewed-on: https://review.typo3.org/55703
Tested-by: TYPO3com <no-reply@typo3.com>
Reviewed-by: Nicole Cordes <typo3@cordes.co>
Tested-by: Nicole Cordes <typo3@cordes.co>
Reviewed-by: Jigal van Hemert <jigal.van.hemert@typo3.org>
Tested-by: Jigal van Hemert <jigal.van.hemert@typo3.org>
Reviewed-by: Alexander Opitz <opitz.alexander@googlemail.com>
Tested-by: Alexander Opitz <opitz.alexander@googlemail.com>