I've been having some problems with TG transit as well, and I believe this is the reason:
It "opens a hole" the size of the ship that mounts the engine, and sustains it long enough for a few more ships to transit through (how many is based on the research tech), given that they are no larger than the "hole".
Why is the hole the size of the jumpship? The jump drive's the one responsible for the actual jump, so why isn't the hole the size of the drive's Max Ship Size instead? It's something to consider: one shouldn't need a 50000-ton tender to assist other 50000-ton ships if the technology allows for drives with enough Max Ship Size mounted on much smaller vessels.
The game mechanics reason is that Steve didn't want to allow small ships with large jump drive capacities to be possible. He wanted big jump ships to be a requirement, thus he created the game mechanics so that the limiting factor was the size of the jumpship and its jump engines, not just the engines.
Kurt