As to the mipmaps, there's an engine function to calculate them, but of course it's faster when they are already stored in the HMP file. They also have better quality dependent on the filter that you use.

The image in the HMP file is stored in straight 888 format. Only when it's loaded in your video hardware, it gets a different format such as 8888.

As to the questions 1) and 5), I've forwarded them to the developer, who will answer them when he's back next week.