See https://discourse.phabricator-community.org/t/upgrade-from-sep-30-2016/3702/. A user performing an upgrade from 2016 to 2020 ran into an issue where this setup query is overheating.
This is likely caused by too many rows changing state during query execution, but the particulars aren't important since this setup check isn't too critical and will catch the issue eventually. It's fine to just move on if this query fails for any reason.