I haven't flashed my phone (yet) but I did upload some flash themes using XS++. XS++ and setool2lite both recognize the phone and can query its properties.

You're right that it's not a great solution, but at least it means you don't have to reboot. If you're hardcore you could check the se-nse forums. I think there may be some example code for doing some of this stuff available in the r&d forum, or somebody might give you some if you ask nicely.