I've certainly joined a pilot-less ship to save them only to find I didn't actually join as a pilot.
Manually clicking the pilot button in a lobby does nothing in a normal crew slot, and clicking the captain slot itself switches you to pilot class automatically. For this reason, you're never really prompted to ever click the pilot button as a manual adjustment.
Joining into a running match in the captain slot ought to automatically switch you to a pilot. It could also bring up a prompt exactly like what has been implemented when attempting to join as a second pilot, warning you that you will be switched to pilot if you agree.
It all seems so simple, and the mechanics already exist for the most part. It's like Muse only ever goes a quarter of the way to fix oddities like this.
