src: use correct microtask queue for checkpoints

I missed in c6c83374 that we should not just use that queue for
enqueuing microtasks, but also for running them.

Refs: https://github.com/nodejs/node/pull/36482

PR-URL: https://github.com/nodejs/node/pull/36581


Reviewed-By: Colin Ihrig <cjihrig@gmail.com>
Reviewed-By: Gus Caplan <me@gus.host>