I think the players won't be faction locked, so the job board idea would work treat as a quick key hub with selection options.
For example, I hit U, it opens a social tab with available missions, I pull down a bar for profession selection, select gunner, pull down another bar for a faction, Anglean, pulled down another bar of selections for w/ mic or without.
This brings up a selection of current missions. Missions displayed would be similar to what we have now, green is in progress, red waiting for crew. Captains would have the option to set a lockout timer for in progress maps, to prevent a quick join. I'd say increments of 1m upto 5 minutes. If a map has an active timer, needs a gunner, you can join and you'll be instantly transported to that ship from your present location.
This is however, temporary, as when the mission is over you'll go back to the city from which you left when taking the job. This will allow crew to join ships all over the world at any time.
This however would not be true for ship captains. A ship would have to be physically docked at a location in order to select an available mission from the city proper and execute it.
With players other than captains being able to join any ship anywhere, this prevents the problem of captains not being in the same location as their ship. You'll always move with your "ship inventory" when you move from one city to another, either as a captain on a mission, or ad a sign on crew for a transport taken as a preformed crew rather than using a quick join feature.