The merge queue should absolutely be bypassable for branch creation - this is a gap in GitHub's implementation.

Quick fixes:

1. Best option: Use your alternative solution - block pushes to gh-readonly-merge-queue/* instead of blocking all branch creation. Since those branches are read-only anyway, this gives you the same security with working merge queue.
2. Target specific branches: Replace "All branches" with explicit patterns that exclude gh-readonly-merge-queue/*. More work to maintain though.

The bypass list not including merge queue operations is honestly a design oversight. I'd file a GitHub Support ticket - this is a legitimate use case they need to address.

Your security model makes sense (restrict CI secret access while allowing PR approvals), but GitHub's tooling isn't quite there yet. Go with option 1 for now.

This limitation comes from how GitHub enforces branch creation restrictions. The merge queue needs to create temporary readonly branches, so if branch creation is globally forbidden it gets blocked unless the Merge Queue App is explicitly added to the bypass list. The practical workaround is to allow the Merge Queue App in the bypass list or, alternatively, restrict pushes only to gh-readonly-merge-queue/* instead of blocking all branch creation. That preserves secret isolation while keeping the merge queue functional. Out of curiosity, were you able to make the Merge Queue App appear in your bypass list, or is it still missing on your side?

• Fwiw, I opened restrict-creations should warn about compatibility with merge queues github/docs#45334 since you shouldn't have to search the community to find out about this quirk.