Move all possible metadata transformations during upgrade (currently done on _userCollectionsWorkForUpgrade and _upgradeServerMetadata) to the new phase added by SERVER-119485, which runs after target version features are enabled.

This will close the race conditions where this interleaving is possible:
1. Existing old format metadata is transformed.
2. Since the feature is still disabled, an operation persists new old format metadata.
3. The feature is enabled.