I would call and speak with a reputable Dynojet represenative about your concerns. Personally from all of the discussions i have had, and real world experience on dyno's and with many many other people with dyno work; the maps made on the dyno void of "ram air" and other real world conditions as you call them; still work perfectly.
One thing i was told my the dyno tuner is that it is truely difficult to take into account ram air. As if you are in 5th gear at 8,000rpm; or 2nd gear at 8,000 rpm the "ram air" effect is going to be quite different as the velocity of the bike in 2nd or 6th at that rpm is going to be extremely different.
That said, unless you have the ability to build independant maps for each gear (as some Yoshi EMS units could do i think), doing what you are wanting to do may not be practicle because of the air pressure differences of different speeds.
Not sure if that makes any sense.
But mostly; the real world applications ive seen are that bikes tuned on the dyno by someone who knows what they are doing run quite well. Hell; bikes with a generic "exhaust" map run quite well.
Hope this helps shed some light for ya.