Well for starters its not hard at all to hit targets at 500 600 700 yards, just takes practice and learning your weapon system.

Yes(and no) your projectile will drop 48.9", but like you mentioned there are many variables that will play into that, wind, humidity, pressure, altitude....etc.

Where is your rifle sighted in at, you mention it hits 3 inches high at 100 yards so what yardage did you sight in at. I always sight my rifles in at 100 yards then I compensate from there. You say 1/4" but is that for 25 50 or 100 yards.