You are looking at a stock equipment profile written around a 5 gallon capacity pot (as described in the notes section). I am guessing that you have not customized much this yet to match your equipment and process. The key factors to focus on are the numbers you can edit and change in the profile. The approximated calculations are there as a guide so that as you customize the profile to match your process you can see estimates of these values. In themselves, they mean nothing until you apply your equipment profile to a recipe.
So where you have an arrow pointing to boil volume and post boil volume, realize they are there to guide you in setting up your profile. The software has no clue your boil kettle is 3.5 gallons and it is up to the user to adjust the numbers to have the values fit their process. If it fits in the equipment profile, you have a good chance that it will work for the majority of your recipes. So your goal here is to adjust your top off water to the fermenter to get the boil volume down to below 3.5 gallons, if you are producing a 5-gallon batch.
