Squash list of `cross-database-modification-allowlist.yml`

What does this MR do and why?

Fix obvious items and remove already resolved items from the list.

This is a small subset of the !74735 (closed).

MR acceptance checklist

This checklist encourages us to confirm any changes have been analyzed to reduce risks in quality, performance, reliability, security, and maintainability.

• I have evaluated the MR acceptance checklist for this MR.