Ahh yes, the physics of speed
First off, 0-60 is probably not the best view of power and acceleration for a motorcycle because most have such a higher power to weight ration than cars there are little tiny things coming into play that can make results less meaningful. Looking at 1/4-mile times and trap speeds are a better indicator (higher trap speed at the end is a sign of higher horsepower, higher at the 100ft is of traction). A huge factor is knowing if both bikes being compared were able to hit 60 in 1st or 2nd gear and at what point did the shift occur and with what method. Assuming two bikes using the same gearing, rider, and shift points even with compensation for standard temp and pressure the variables get persnickety at these minuscule time differences. Basically everything is impactful...including things that we may not think about, like: viscosity changes in the fluids in the driveline; overall rear tire diameter changes because of brand/mdel/size change, altering final drive ratio; the shape and delivery of power within the rev range; materials and condition of the clutch; materials and condition of the brakes (any drag will come into play); suspension geometry and setup (this is actually huge as it effects directly the ability to transfer power to the rear). Then their are the operator components. Big ones include skill at launch, throttle and clutch control, experience level and feel. Then come environmentals including: track surface; surface and air temp; humidity; composition of the launch surface; direction of wind; etc.
The changes that were described are major in terms of power delivery. The fly-by-wire combined with throttle body changes are probably creating much more clean power pulses, smoothing out delivery. Also, the mapping change and throttle bodies likely impact the low and mid, important for good launches. The suspension change can increase the mechanical traction available to the rear tire, again providing a stronger launch.
My guess is that it is making up the time in the first 1sec to 2 secs of the run, where weight isn't much of a factor but the ability to deliver a strong launch and faster transition to full throttle is.