Tuning is tuning. If the ecu your dealing with only does fuel, anyone with a well calibrated dyno/AFR read out can tune it correctly. Its not rocket science… and it is no different bike vs car vs truck vs kart vs boat vs 4 wheeler. its an engine. SURE it has twice the revs and smaller displacement where +/- a few % will make a larger difference than a large displacement slower revving motor, thats understandable. A 1000 CC motor sucking in +2% more fuel and going from 14.2 to 13.9 for example, is like a 300Ci motor which has say a 8-10% window to make the same AFR change. you can be +/- a few clicks on the V8 and not really see a change, where +/-a few click will send you off the scales on a little motor. Its simple math that proves that.
Not to mention, a quick search for GSXR1000 showed me a full page of files for different exhaust/filter combo’s Dynojet already tested for you, with their professional tuners, that I bet can out tune about any local guy around. Granted environmental changes and all effect it but it will get you more than in the ball park, if not running around the infield.
So what is this bike exactly anyways? Whats done to it? What level rider are we talking? Where do they ride? What are their goals?