Given the fact that combat is fleet-based, I don't really see the validity of your explanation.  Transports add nothing to a fleet, already putting you at a disadvantage in fleet on fleet combat.  Then you have the fact that there's no zone of control exerted by fleets- so even if you create screener fleets for your fleet loaded with both combat ships and transports, the enemy can just zig straight through them to get at the weakest fleet.  Given the massive move advantage in their own territory, the entire gameplay logic falls apart. 

Further, it simply makes no actual sense for a transport fleet to be the one attacked first when an enemy attacks a hex you occupy. It's so counter-intuitive that I actually was shocked after a year of playing to see it happen.  Why would two fleets sitting next to each other choose to intercept an attacking force with the defenseless fleet? 

Don't take my disagreement with not valuing your response, I just don't think it's valid. 

IRL the transports wouldn't engage with the enemy. In space you can see the enemy advancing at great distances. Either the escorts would advance to engage leaving the transports in the "rear", or the entire fleet would turn tail and try to flee if the fleet commander determined it would be a losing battle. That said, if the attacking fleet was faster than the defending fleet, they might be able to catch the defenders before they can do either, and if they are trying to flee then they should not be engageable in the month of the first attack, but on the subsequent turn they would not be able to able to disengage. I hope that's clear even if it is a little convoluted.