It doesn't really matter what the sailmaker's software says. The real question is what does the sail measure. The class rules need to state the procedure for measurement, and what the legal values are. If they don't, then the class rules are lacking.

For example, I sail in one class where the luff, leech, and foot of the sails are measured under a specified load. There are minimum and maximum allowable lengths, and maximum chord depths at the midpoints. As long as those values are met, the sail is legal - regardless of the actual area.

As others have noted, sails are pretty much always measured flat despite the fact that modern designs are 3-d. The area we measure will be different than the modeled surface area.

Also, when the bolt-rope (if any) is sewn in, it will be made short in order to allow for stretch. If the sail is measured without proper tension on the bolt-rope, the area will come out significantly smaller. As a sailmaker and Isotope class measurer, it took some time to work out assembly and measurement procedures such that the numbers before and after attaching the bolt-rope matched.

Also, realize that sail measurement is not an exact science. Measure the same sail twice and you'll wind up with small variations in each value. I figure that my margin of error is at least +/- 0.5%, so if the sails measure within 1 sqft of target (total), I call them legal.