Software updates are covered under warranty if there's reason to believe the update will fix an issue you're reporting, like an SIB for said issue. Otherwise you pay for it, and if you're outside of warranty you pay for it regardless. I understand the "If it ain't broke don't fix it" mentality too, but I agree there must be some reason the software got updated, and I doubt it's always "just to support new models/options".
As far as dealers being reluctant to install updates, I understand the dealer's viewpoint that a botched update would be very bad, but if dealers are so worried about installing an update I think BMW needs to come up with a more reliable updating mechanism....
OP if you're loading ESS software (not sure whether you mean just a tune or the software for their supercharger) just tell them why you want the update and pay for it. The update isn't to fix an issue covered under warranty so even if you technically COULD lie and get it done for free, you're certainly not entitled to it given the reason you want it. And you're going to lose your warranty on that part of the car by going ESS anyway, so there's no point trying to be shady about the preparatory update. Unless you plan to try to bring everything back to stock later if something goes wrong and come to the dealer saying, "Yeah I don't know what happened, it just broke....", but we already had a thread about that a while ago:
http://www.e90post.com/forums/showthread.php?t=592140