An important factor in this kind of an exercise is understanding how actual bullet trajectory over its entire flight compares to the flight path predicted by various ballistics calculators. I have always used JBM for a number of reasons, but mainly because it satisfies my specific needs. I noticed early on that its predictions with the loads I was using seemed to be very good out to 300-400 yd, and also at 1000 yd. However, the region from about 500-700 yd was where the predicted drops didn't seem to match up very well with real world drops. Because the predicted drops both closer and further from that region were basically spot on, I don't believe it was an issue with bullet BC or velocity, but rather something to do with how the calculator predicts/calculates drops. In other words, the predicted trajectories for my loads were mostly spot on, but were slightly off in the middle to slightly past middle distances. For that reason, using a distance in the middle range to "true" up the entire trajectory could well have thrown everything out of whack.
One issue with using actual drops at a specified distance that must be considered in this type of exercise is the starting zero at shorter distance (i.e. 100 yd zero). As an example, let's say someone has zeroed their rifle at 100 yd, shooting a half-MOA group. The elevation turret setting that produced that half-MOA group has already potentially introduced +/- ~0.25 MOA variance into the mix when subtracting it from the average elevation required at some farther distance (i.e. measuring drop). Thus, establishing the short range zero as tightly as possible is important when carrying out this type of exercise. Likewise, wind conditions that affect elevation at distance, mirage, and a few other factors can come into play.
Since I acquired a LabRadar a few years ago, I have extensively used the velocity differential from 0 and 55 yd to estimate bullet BCs, again at JBM Ballistics. I do this largely to compare various bullets, pointing methods, etc. It is worth note that 55 yd is far from ideal in terms of velocity drop because the magnitude of the velocity drop is much smaller than it would be at something like 500 yd. This has the potential to compress the y-axis of a graph of velocity versus distance, rendering BCs estimated using such data to potentially be less accurate. Nonetheless, I routinely generate BC estimates for unpointed bullets that are spot on the box value. Further, pointing bullets will yield the expected ~4-6% increase in BC. Finally, when used in combination with measured average muzzle velocities, these "estimated" BCs seem to provide pretty good drops at various distances. My point here is that there is typically more than one way to generate a drop chart. If actual drops do not agree well with predicted drops from a ballistic calculator, it may be worth checking or comparing using a different method. In general, the more information you have, the better off you will be.