I think it would be a bad idea for CL to exclusively tie themselves to a proprietry file format. Which one would they go for? Whatever they chose, the majority of people would be pissed. Plus there is always the problem with copyright infringements (aka GIF).

At the end of the day, the total amount of information (excluding headers) required would be the same whether it is packaged into one or more files, but with less flexibility in using some lower res components to save memory.

My vote is with the open file formats - do any of these support multiple layers?