I'm sure I've had results from ad-hoc queries submitted using the UI logging to those files in the fleet config

This has never been the case in Fleet. Live query results always go to the UI (or now fleetctl) and never to file on the server.

uh, I must have got mixed up. What results are logged to those files? Scheduled queries?

Scheduled queries are logged to those files (assuming you have configured osquery to use TLS logging)