This may be "old news" but it's worth noting that it's still very much an issue. I had my 1,200 service yesterday, and while I went over the items in detail for the service with my SA the mechanic actually only did the diff and engine (not the transmission).
I questioned that, and was very happy that my SA took time to look into it, did some research, and acknowleged they'd missed the transmission. (No hassles, just a postive we messed up what can we do to fix it attitude--that goes a long way with me.) They're dropping off a a loaner to me and picking up my car so that the hassle is minimized. Of course, one time at the dealer would be preferable but they're going the distance to remediate the problem with grace and a good customer service approach--so they still have a very happy customer.
As mentioned above the checklist the mechanics use doesn't have the steps clearly outlined. And most of the cars serviced at my dealer are DCT (no transmission service req'd). So, it's pretty easy to see how this can be overlooked--not to mention the dealer had over 40 cars in yesterday for service...and M3 MTs make up a very small % of vehicles that come through there monthly (if not annually).
Recommendation: In retrospect if I had it to do over again I'd have printed a copy of the SIB from the OP. I'd have reviewed the copy of the SIB itself with the SA; and asked that she staple a copy to the work order. I would have added a little note along with the SIB saying "you probably know this already, but this seems to be a common issue due to the BMW checklist, just FYI"--don't want to piss off the mechanic. While that may not be something we "should not have to do" I think it would go a long way to help avoid this issue for others. I suspect most dealers/service depts. want to do the right thing but the protocol/steps and service volume make this not clear to them and a reminder done in friendly manner might help. Hey, this approach is worth a shot--nothing to lose.