I, too, have no problem with alpha channel in panels. Look at my 2D game's clouds once or the scene in general and nearly everything you see has alpha channel (the sky (not the space effect) and the ground don't). In fact, my 2D game is likely the most extreme game made with panels as there are over 200 of them!

My latest screenshot available
A second screenshot - near the ground

The clouds have varying transparency, the edges of the mountains have it, practically all objects have it (except the hills as they don't as they need to be redone anyway - they're from version 1.x).

As to publishing, if you have Pro edition, resource it. If you have a lower edition, look into getting some file packer. Molebox is a great one to look into. I use it. Not only does it encrypt files, but it also compresses them.