My dealership is pretty mod friendly. I had a recall done and forgot to take out the JBD. All the tech did was unplug it, do the reflash, and plug it back in.
The only downfall to the JBD is the once a month (atleast for me) limp mode and code. I have mine at 100% and it occasionally throws a limp mode under acceleration. I just went out and bought a Scanguage 2. It clears codes for me on the spot and stays plugged into my OBD. It also serves as a temp readout and a few other stuff.
Mods: AEM Meth Injection, BDP downpipe, Wagner intercooler, Bilstien B12 Kit, M3 Control Arms, MB Quartz Kit/Alpine Amp
Best 1/4mi: 12.34s @ 111.88MP/h