You definitely need to field check your specific load versus the THEORETICAL data provided by the calculator. The beauty of the calculator is that it tells you what to expect from a specific load, so that if you aren't getting it, you know something is different with your load (ballistic coefficent, velocity, etc.). For instance, one of my pet loads was supposed to shoot 1.5 inches high at 100 and zero at 175 yards. After sighting it in at 1.5" high at 100 yards, I checked zero at 175 and found that it was shooting almost an inch low. Not having a chronograph, I didn't know the exact velocity. Plugging back into the calculator different (lower) velocities and zero distances (around 150 yards or so) until I came up with one that was 1.5" high at 100 and -0.8 inches low at 175. Turned out I was about 125 fps slower than I had thought. Using the correct velocity, I was able to zero at 175 yards by raising my 100 yard sight-in by about half and inch.
I don't use the + or - 3" PBR as it is on the calculator except for long range (+200 yards) situations. The 3" high could result in a poor hit on a whitetail at 100 yards (just under the spine instead of midway of the lungs). I prefer to keep my personal PBR as + and - 2" instead of their 3". Less room for error, and at less than 200 yards I can hold dead-on with confidence. It just means a larger holdover at +200 yards, but I rarely shoot that far, and as long as I know where the holdover should be at a given range, the actual distance of the holdover is academic. I keep a holdover chart for ranges in 50 yard increments out to 400 yards for my load at the appropriate zero taped to my rifle stock while hunting. It doesn't read in inches, but rather in positions, like "midway" for halfway between brisket and back line, "spine" for 3/4 from brisket to backline, "1/4 over" for a point of aim about 4" above the backline, etc.