Hopefully it's alright to post this here since it hasn't been too long since the last post.
I've been having the same problem the original poster had with this, where I move a selection and try to fill the empty space and it's treated differently, I had the problem on 4.0 and after updating with the fix. Right now a new layer is transparent white, a deleted area is transparent black, and the area left over after moving something is your secondary color but transparent. It seems like it'd be easier to work with if they all used one set color like black with an alpha value of 0.
I'm not sure if it's just the type of work I do, spriting and such, but it's been coming up often where I have to keep deleting a lot of empty blocks of space that use various transparent secondary colors. If it's useful for some people to leave it as it is maybe there could be an option that lets you either use the transparent secondary color or transparent black?
