To be honest, I hadn't thought of that potential problem. On my rig I have lazy jacks and a boom bag which probably has enough room. But this may not be the case for everyone and your point should not be overlooked. I'm probably a loooooooong way off from making this move. Hope I don't forget this when the time comes.
The issue is with the diagonal batten at the top. The sail won't stow in your boom bag unless you remove the batten each time (re-insert before raising). That extra time/effort might get old in a hurry if most of your sailing is just casual daysailing and cruising. How much is that extra 10th of a knot worth?
2 Hulls look at the following possible solution for your square top main by CT battens from New Zealand. http://www.sailbattens.com/documents/ct_air.pdf
These battens are air pressure filled battens that can fold so maybe that could solve the problem in getting them in the lazy bag.