Resolve "Not seeing "mentioned in commit" system message after merging"

What does this MR do?

Fix a regression in master (but not yet in a release). When we merge a commit using the default commit message, we don't want to close any issues twice, but we still want to generate cross-references.

Are there points in the code the reviewer needs to double check?

Don't think so - the second parameter to #create_cross_references! is confusing, though.

Does this MR meet the acceptance criteria?

• Tests added for this feature/bug
• Review
  • Has been reviewed by Backend

What are the relevant issue numbers?

Closes #43809 (closed).