So... this isn't the first time this has happened, but it's still frustrating, and should probably be fixed sometime.
I decided to join a lobby my friends were in. I managed to pop in with less than one second before the match started -- in a random slot, on a random ship... still in my pilot role from earlier. At no point did I actually /see/ the lobby screen.
So, now I'm stuck as a second pilot on a ship. My options are pretty much increase our odds of losing, or take a Leave. Abandoning and rejoining the match doesn't allow me to change class (and, IMHO, is a bit of a cheat anyways) -- I'm told I can find the lobby through the match list, but I didn't catch the name of the lobby either (I joined via friends list) and, still, I think that's a bit of a cheat.
There should probably be some sort of deal to fix this -- perhaps a (partial?) reset of the timer if someone joins the lobby in a ship slot, and/or a preference for having people who join during the timer go to spectator slots. The former would at least allow time to react (and leave with no penalty or adjust correctly), though there's the risk of a match never starting if someone repeatedly leaves/joins (there's probably a way to fix this.)