ROFL!!!!
This is a brilliant reverse-justification for an anti-micro-management convenience feature (the standard transit) that was always a little fuzzy in terms of precise game mechanics and is now causing confusion. The most ironic part of this is that I suspect, with the new fleet organization stuff, that the standard transit could have been eliminated in favor of Aurora automatically managing the transits of the sub-groups (note that I am NOT advocating the elimination of standard transit in favor of this). I salute you, sir!!
One suggestion: Do you want to explicitly state a 3rd, "Bridge" mode where the Jump ship is positioned on the WP (and not part of the transiting TG) but is otherwise equivalent to the standard transit. There could also be technobabble that while the wormhole is open for bridge mode, the jump ship can act as a comm relay to both sides of the WP? The advantage of adding this statement is that it makes it explicit that the jump ship is on one side of the wormhole and isn't popping back and forth in a way invisible to the player. In fact, maybe the standard transit order should actually be explained as having a jump ship in the TG open a bridge, then close it down after everyone's transitted.
Another suggestion/comment: Should jump gates only allow a "bridge" (standard) jump? I think you mentioned a while back that they have a zero jump radius, so this would just be more exposition on what's already going on. That way there would still be an incentive to give a TG a combat-transit order if there were an enemy fleet on the far side of the WP, and it would be explicit that such a combat transit would require and use jump ships in the TGs.
John
