Fix issue with the `default_merge_refs` feature flag removing version to version diffs

What does this MR do?

As per @m_gill 's explanation here - Fixes an issue where comparing two versions of an MR diff was not accurate when the default_merge_refs flag was enabled.

Screenshots (strongly suggested)

Does this MR meet the acceptance criteria?

Conformity

• Changelog entry
• 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.
• Tested in all supported browsers
• Informed Infrastructure department of a default or new setting change, if applicable per definition of done

Related to #276917 (closed)