I've moved this thread to the Ext Dev forum because the extension isn't Flash only. It just happens to support Flash. Btw, upcoming Beta soon. Because of personal reasons, this one will have no Flash though. I can't work on Flash at this workplace I'm afraid.
1) Yes - In fact, after discussing with some clickers, I've decided on a format: Basically, it's already there! You can just have an invisible layer, storing your collsiion tiles, and check for collision with it. That's it. Super flexible.
2) I've actually sent Yves a PM about this. I could implement this in Flash *easily*, but not in the EXE version. It'd require some hacking, I hope he can help. Nevertheless, I will offer this feature for Flash, even if I can't implement it like that in the EXE version. It's just a single property, anyway (render above player, yes or no). It is possible to put the Tile Map above an Active right now, but you can't do both behind and above at the same time with one instance. I might offer the ability to link a second Tile Map object to another one so it can render some layers above an Active.
3) Yes, that's one of the major advantages that I forgot to mention in my post You can do that of course.
I think you might like this extension