I figured this out yesterday. I spent quite a bit of time messing with it, but ultimately, it's quite simple. As you said, you start with mapcruncher and the tiff of the chart. You recalibrate it and let map cruncher do its rendering into tiles. And then what you're left with are tile files in the same format/naming convention that Virtual Earth uses internally. So what's left to do is roll your own Virtual Earth style map repository, which can be done simply by dumping the tile files into a directory of a handy web server and creating a repository in Maemo Mapper. I have a web server running locally on a computer on my home network with an address of 192.168.0.9, and the tiles are in a web server directory called tiles, so the url looks like:

http://192.168.0.9/tiles

and the Maemo mapper repository url looks like:

http://192.158.0.9/tiles/%0s.png

Then I used the maemo mapper auto downloading to pull in the chart. Using another repository, I navigated to the chart area, then switched to my chart repository and scrolled around to bring in the chart.