You got to ask some questions and now I have some for you.
Before you fire the first shot in developing field data and drop charts the only givens you have are the accurately measured field weather data that you have measured and put in your software.
The next given is the muzzle velocity, accurately measured, hopefully, with your chronograph. After that all else is developed from actual shooting and developing of field data and drop charts.
Question 1: Do you know what happens to BC when velocity changes?
Question 2: Do you think that constantly changing velocity, and therefore BC, would cause you to possibly chase your tail in field shooting?
I believe you'll find that most will accurately chronograph velocity at a given distance from the muzzle, then using that data and all pertinent field weather and environmental data continue and by shooting develop drop charts.
I believe you'll also find that most will juggle the BC number in their software to get their software calculated data to match up with real world data proven by shooting. Even if you start with a manufacturer stated BC you never know what it actually is in your gun under the current field conditions until you shoot it and develop true data.
I guess to answer your question I'd say that the data for muzzle velocity that I put in my software is the actual velocity from my chronograph testing and if I tweak any number it would be the BC to make everything match up so the software can then give me reliable first shot data.;);)
Even when all matches up at say, out to 800-1000 yards, I'd also suggest that you check actual drops by shooting out to the absolute maximum ranges that you'll ever shoot. You may find that you might have to make some slight adjustments at extended ranges.;)