This has already been suggested once a million years ago, where matchmaker wasn't even a word that could appear in anybody's dreams.
Matchmaker should avoid half empty lobbies like these when people are queueing up, but they may have made the custom lobby themselves or wanted to play a specific map, as the map is different or matchmaker just flat out failed. But maybe, there is a ridiculous gap in the total MMR between these two lobbies, so the players didn't get into the same lobby. Four veteran friends or clan members crew formationing is not that rare, after all.
Schwalbe already mentioned that you don't know what position they are all in, it could be two full ships in one lobby and in the other 4 pilots and the rest scattered around the lobby, who would keep their position?
But I wouldn't oppose the possibility of matchmaking giving the players in these lobbies a vote, wether they wanted to merge into a lobby with other players, giving them a warning that they may be on a different ship and would need to swap with other players to be back in their original position or if they wanted to stick to their current lobby and wait for it fill up naturally. Only opening up the vote if the lobby has been waiting for a significant amount of time.