An update... I've now driven 18,000 miles with the actuator unplugged, a small amount of which were with a JB+. I've been to the dealer a few times for routine service and miscellania (top off coolant, burned out halo bulb) and no problems.
Never had a visible could or SES light.
Got an AP today (which I know isn't as good at reading codes at a BT cable, from what I understand), and no codes with the actuator unplugged.
I'm sure there is some random little code that is thrown, but I'm also pretty sure no one at BMW cares about it.
BTTGMan's post was interesting. There just seem to be an awful lot of good, technologically advanced turbo cars out there without this. I agree that BMW is detail oriented, so maybe there's a reason... Then again, the windows dropping 1/8" was brought up, and to me, that's an unnecessary detail and not necessarily a testament to them. You can build a frameless door that has just as good of a seal and doesn't need the window to constantly slide up and down like that... those of use who had WRX's know...
(the WRX's entire door seemed to move up in the last millimeters of closing, such that the glass went below and then up under the "rim."
Bottom line regarding this "mod": It's not a big deal either way. Try it and see if you like it. If you don't, or you're even a tiny, tiny bit worried about it, then just don't do it. You're not missing out on that much. But if, like me, you think there's zero problem with doing this and you do like the very, very subtle change in exhaust note, go for it.