It's likely that some folks would've stretched to afford the 3E/3A fares instead of boarding connecting trains via Mumbai, because the latter option would still be more expensive than SL fare for direct journey in this train. For a means of public mass transit I don't think it's correct that people should be forced to cough up the cost of AC classes by doing rake standardization, such long distance train journeys aren't a luxury for most.
Also regarding the question of running an Antyodaya train on this route, it could be argued...
more... that such a train would make quite some losses too, if that's the logic behind rake standardization of regular reserved coach trains.