oh. that's why mobi files created by kindlegen are so much bigger than those made by calibre. i'm going to try a few conversions right now!
pipe-dream: may be amazon believes that most/a lot people will be using kindlegen to convert epub to mobi. so, if the mobi contains the epub source, it will be much easier for amazon to put their weight behind epub if that day ever comes. did i mention this was a pipe-dream?