The best way to have a single scratchbox setup and multiple targets is to just point apt to the official scratchbox repo and download most packages (you can pickpoint which ones you really need, of course). Then configure each target manually. Fortunately, Nokia still provides manual install instructions for most targets. I've run all Maemo versions this way.

Also, sometimes you have to clear ~ when switching between targets. Not very often though. There's a gconf-clean.sh script that seems to do a pretty good job.