Of course if you spawned in the last known position, you might find yourself sitting in the same chair as some NPC, etc.
They seem to keep track of the position while the carrier jumps, but I've also come out of a jump sitting in the same seat as a commander that was in a different instance when the carrier jumped, but we both ended up in the same instance in the same seat. In fact there were quite a lot of oddities when we tried to jump many commanders on the same fleet carrier, i suppose mainly due to instancing issues.