I've newly tried (after many hours as it is).
Setting the MXML spark Application properties for alpha=0 visibility=false and then when the application completes restore them. (NOP)
creationPolicy for the Application all (NOP) none (NOP) auto (NOP)
Still it always flashed the backgroundColor (of black in this case) right before the transparent or whatever background of the assigned skinClass kicks in.
(Which will be needed for fullscreen edges).
If you leave it out initially it can not be assigned after the skinClass is (so white edges in fullscreen mode result).
Setting width and height to zero or one and adjusting later also not an option. (This is embarasing but I've mentioned how I would have made it and expected it to work [this has to be a bug or lets call it oversight I'd love patched, thanks.])
Maybe there's a way to programatically make/create the really application object and then drop it in to the other one (after the background is assigned and the skinClass kicks in, so the edges in fullscreen are not white).
Is it just me or isn't this the first thing everybody does and sees it doesn't work properly (I mean we arn't past the background working right yet here)?
I'll try this next...
but it will probably lock&crash the browser (cause debugging fullscreen is a nightmare too) so maybe I'll post more failures after that, getting tired now though. (NOP didn't help either)
Seems to be issues with wmode trasnparent in some situations still aswell.
I might find a way to draw off screen on fullscreen event down the road as a lame patch for now.