I can't accept that he is saying they can not account for zero speed input because of the fact that it can be tuned on the PCM for zero on manual transmissions with no VSS input (2wd or otherwise) and then it will not have the idle stop/cut out I think you are talking about. I am going to make a recommendation you reach out to a tuner at LSX Specialties (You'll have to look them up on facebook if you want instant message access but that is the easiest way to get ahold of him). Alternatively he has a phone @ at 541-821-2993. Like your tuner he has mail order tuning and should be able to understand the feedback you offer and give an opinion on the matter with no cost involved and he has been very helpful offering feedback on tuning matters.
Also Just curious what VSS unit you are using? I think I know what it is but knowing might help me ask a couple of questions across the spectrum of tuner friends I know. Alternatively, if you are not already subscribed, get on facebook and get into the group named LS Swapped Square Body GM Trucks ('73-'86 C/K & '87-'91 R/V) and ask for some opinions as well. I've found that one tuner may not have an answer but you might get a lot of feedback there if you can filter through it all and also maybe get access to a part that you can use instead of swapping a hole transmission because once you go that route you will also be having to have two driveshafts adjusted as well as moving your t-case shifter and cross-member..