I didn't read anything in to the Loftwings being beneath the barrier, i was just happy that the game had ended. However SS was full of things like that. Under the cloud barrier it shouldn't have been a wonderfully sunny day on land. I'm aware that the whole province was visible from the portal so it was obviously a large break but something like a cloud barrier should have been seen in the distance.. but there was nothing.
Also, the thunder dragon can't die but can get ill... fair enough, so then why do we see his skeleton on the ground before we activate the time shift crystal in the Gorge?
Perhaps the cloud barrier thing was as simple as, Demise defeated means no need for it and it cleared up immediately... it definitely went at some point since no other Zelda game has it, so why not then?