Geo: Fix duplicate Package File Registry rows

What does this MR do?

Fixes a race condition where duplicate Package File Registry rows could be created, which would cause incorrect counts in UI and rake task status output.

Resolves #321945 (closed)

Does this MR meet the acceptance criteria?

Conformity

• [-] Changelog entry => behind feature flag
• Documentation (if required)
• Code review guidelines
• Merge request performance guidelines
• Style guides
• Database guides
• Separation of EE specific content

Availability and Testing

• Review and add/update tests for this feature/bug. Consider all test levels. See the Test Planning Process.