I always give any large UFO that looks like it might land a flyby before it does so. If it is an abductor ship, it is reasonable to assault. Transports have those massive outsider pods and terrible cover so I generally don't take those missions until I get ghost grenades.
Sounds reasonable, I think this was a transport ship. Spawn was directly outside the massive opening with the cross-shaped second level with the grav-lifts. And it was loaded with pods such that, when trying to take any of the limited cover between me and them, several outdoor pods from the decks on either side were activated.