I dont think you can leave it in. It is very tight in there when the window mechs are moved outward. The lower part of the runners neeed to be as far out towards the skin as possible to make the glass curve correctly inwards at the top.
Leaving the bar in isnt going to gain you a great deal since the door latch is attached to fibreglass rather than metal tieing it to the latch. In a side impact without the other end tied to the latch, it wont do you any good.
On the next one i will be trying to get the windows in and working with the rubbers fitted before bonding the outer skin if possible. I would maybe just screw the outer skin on till its all sorted. Depending on how far down you want it to go the outer skin may need a flap cutting in at the bottom to allow the window to come down fully.