I think the speed of a projectile in a vacuum is only important as a reference for the projectile's trajectory without wind restistance. Therefore if you know what it can do without moving through air and what it does on air you have a coefficient to use should you make other adjustments which change the trajectory. Because in a vacuum mass makes no difference to trajectory it means you are simply dealing with speed, distance, time and angle. (If you drop a feather or a two tonne weight on a vacuum they fall at the same speed, it's only air that slows the descent of the feather in air)
Unfortunately like quantum physics dictates the physics in small scale against Newtonian physics, fluid dynamics and statistical particle mathematics are probably more accurate although computationally far more intense. In order to determine though the actual effects you are probably going to need to dial out a lot of possible error in the experiment, the likes of which is probably going to be very expensive and impossible to solve completely. This is why f1 cars can be built on computer, but rely still on wind tunnels and only prove the effects on the track.
For one I'd be thinking about using 2 chronos at the same range distance calibrated to each other to ensure there's nothing odd in the data. It would seem odd that there is something not seen at the muzzle seen at the target but I'd like to rule that out to start seeing as its the source of the data.
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