The FJR odo does read a bit high but the GPS can, under certain circumstances, read a bit low.
1) If you are riding with extreme elevation changes, the GPS gives your point-to-point distance on a flat grid. For 100 miles (point-to-point)with an average 10% grade (quite steep), the error amounts to only about a half percent (100.499 miles actual).
2) The GPS is measuring a whole series of straight line differences between positions. Depending upon the frequency of measurements, it is conceivable that a VERY curvy road would yield a slightly lower than actual distance.
3) GPS accuracy for any given point is a function of the quality of the unit but also its dependence on a clear satellite signal. Accuracy is diminished in cities with tall buildings or canyons etc. Less accurate points may have the GPS saying you travelled further than actual.
Having said all of this, there is probably far more variability in mileage as a function of environmental variables (speed, terrain, altitude, ambient temperatures, braking etc.) than there is due to odometer accuracy or GPS errors. For fuel warnings, your odometer and fuel gauge along with your experience with your bike are going to be FAR more reliable than a warning that can only be based upon distance travelled. I know that my actual mileage can vary from high 30's to low 50's MPG as a function of driving conditions. My wristwatch to determine hours per tankful could be almost as accurate as an external distance indicator.
Ross
Edit: I just reread your original post! It seems that you simply want a distance indicator warning to satisfy Iron Butt rules. Yes, it should work OK for that but I think I would just use one of the two trip odometers on the instrument cluster. I would use the odometer in the Zumo for the "Master" distance. I assume you have more than standard fuel capacity - for me, 300 miles is maximum range and only if I'm taking it VERY easy.
