Rocketman I am wondering the exact same thing. I have personally spoke to a couple of guys on BBC who say they are running the Mike Nass alien cowling with no ECU re-flash on a 250XS and have had no issues running lean. They have checked the plugs several times after running, but I feel a little scared to take that chance. I even asked Mike Nass himself via email and he replied back with the following: I have never heard of it... If the Eco, can't adjust for better air, there is a problem... What if someone ran with cover off... Would it blow up?... I doubt it. I also asked Joe and he said it would run leaner and could be bad. I guess if you can afford the alien cowl it might be wise to flash the ECU as well just to be safe.
Mike also told me you do get denser drier air, so with this available, the re-flash can take advantage of it and collectively makes more power.