DFT Bluetooth requires a custom driver, I believe, so I'm guessing it won't work. That said, being able to support custom drivers on stock ROMs would be incredibly useful...
XapHandler (the Sliverlight/native hybrid app that I'm working on, as opposed to the all-native XapInstaller.exe used by custom ROMs) should be supported, but so far I've only managed to get it to clean-install, not update. That's using HtcRoot, but the effect is similar even though the method of elevation is quite different. I'm guessing it's a bug in the app, though. In any case, I have been able to open and install XAP files directly on my stock ROM, so that should be possible for everybody when WP7 Root Tools 0.9 is out.
Heathcliff74, did you ever decide on a way to trigger an app asking for elevation? For example, if the app were to launch WP7 Root Tools and pass its own GUID as a parameter, you could show a UI asking the user if they trust the app? Just a cool idea that would make the experience a little better, not at all something worth delaying the next release for.