It's very much like using an IBU calculator. You're not likely to hit the measured number. You're probably not even particularly close. But you need some sort of benchmark for measuring your initial conditions, and some way to quantify what changes you make for subsequent batches. The calculator doesn't need to give you a number that equates to anything in the real world. It just needs to model conditions close enough where you can compare and adjust between batches.
One does not need an IBU calculator either. All one needs is a unit of measure because we have no idea if the alpha acid rating on the package accurately reflects that current state of the hops. Amateur brewers used HBUs/AAUs long before IBU approximations became the rage. An HBU/AAU-based hopping rate combined with a boil length is no less valid than a calculated IBU value when it comes to repeatability, and hopping schedules based on HBUs/AAUs can be calculated in one's head.
The same thing can be said about extraction efficiency calculations. Efficiency calculations only reflect reality to point where the dry basis, fine grind (DBFG) or hot water extract (HWE) values used in the calculations reflect reality. These values can change from malting to malting and season to season. Once again, there is a simpler unit of measure available for the job. It's known as points per pound per gallon (or points per kilogram per liter for those who use the metric system), and its directly usable without having to enter numbers into brewing software. If a brewer knows that his/her average extraction rate is 30 points per pound per gallon (the extract from one pound of grain in a one gallon solution has a specific gravity of 1.030), all he/she needs to do to obtain the weight of the grist is to calculate the total number of gravity points in the target batch and divide by his/her PPG value.
Sierra Nevada Pale Ale has an original gravity (O.G.) of approximately 1.053. Our average extraction rate is 29 points per pound. How many pounds of grain do we need to make six end of boil gallons of wort in our brew house using points per pound?
Step 1.) convert the O.G. to gravity points
1.053 = 53 gravity points
Step 2.) Calculate the total number of gravity point required in the end of boil volume
6 x 53 = 318
Step 3.) Calculate the grist weight
318 / 29 = 11 pounds (rounded)
From here, it is merely a matter of breaking the grist down into percentages. SNPA is American 2-row and caramel malt. I have seen caramel percentages ranging from 3% to 10% of the grist. Let's pick 5% for our example.
11 x 0.95 = 10.45 pounds of 2-Row
11 x 0.05 = 0.55 pounds of caramel
Or if we want to simplify measuring
10.5 pounds of 2-Row
0.5 pounds of caramel
It's that easy.