I might be misunderstanding what it's doing, but it sounds like you're getting an "effective BC" given your current conditions.
That would be great for that days shooting, in that location, but it seems like you'd want the "real" BC - that is, a BC that's been normalized to "standard atmosphere" - which should very closely match the "book" value (if there is one). With the "real" BC you can adjust according to conditions where you are at some other place and time. With an "effective BC" you'd have to back-calculate to a "real" BC then calculate a new "effective" BC. This would be a fairly manual process in any of the ballistics software that I've used.
I've never heard anyone use the term "effective BC" before - that's just what I'm calling it. But a BC that takes into account specific atmospheric conditions (other than the "standard atmosphere") should at least be called something different as it wouldn't be directly comparable to the numbers presented by any ballistician.
GsT