[BUGFIX] Fix problem with saving extension configuration in different tabs

The new ConfigurationUtility is working internally with configuration as
valued array, but the existing configuration is serialized in the old
nested format. When merging these two, exising configuration was not
merged correctly, resulting in error where configuration set in other tabs
was lost when saving.

Change-Id: I9007a0f80974A72610b3afc1e1dc76f7cad31fca
Fixes: #42775
Releases: 6.1, 6.0
Reviewed-on: https://review.typo3.org/17720
Reviewed-by: Christian Kuhn
Tested-by: Christian Kuhn