So I found a hack for using Kindlegen to create files for the Kindle that use different sources for the mobi part and the KF8 part - description on my blog at
http://extraordinarycommons.com/crea...erent-sources/.
I'd like it if people could check files generated using the technique and see if there are any problems compared to official files; if there are no problems, a python script (or other tool) to do the same thing in a convenient manner would be very nice.