Hi Dale (I made sure to read your post, and re-read to make sure, lol)
1, as you said this will mess with hit testing, if anything I would advise against that approach, also point 2. as invisible sprites still register with hit tests.
3. "The Game Factory" and "Multimedia Fusion", was built around this approach, you just have a giant area to work with and pan the view to suit the scene you want to display, personally speaking I thought it was naff, but it works, so its a viable option
4. if the "pop up" scene is A not resource heavy and B in use a lot like an inventory, then yeah, move them off screen but you might run into depth issues with the underlying sprites
5. is well, yeah delete it and recreate it each time you need it, again depending on how resource heavy the "pop-up" is...
personally speaking here, I would off screen them and use this as an opportunity for some "eye candy" and tween it, make the pop-up slightly smaller than the screen so you can still; see what's behind and have a fade sprite and tween the *inventory* in ...
kinda like this
