Price per piece treats a minifigure’s components exactly like any other components, which is the measure’s biggest blind spot. A published piece count does include the head, the torso assembly and the legs, but those few items can be worth several dollars together while the same number of ordinary bricks is worth cents. So a set with six figures can look expensive per piece while being good value overall, and a licensed set with no figures can look cheap while offering very little.
One thing to be aware of when you read the bricks-only figure: the calculator subtracts what you say the figures are worth, but it still divides by the full published piece count, because that count includes the figures’ own components and the number of them varies with hair, headgear and accessories. Inventing a parts-per-minifigure constant to take back out would make the number look more precise without making it more true. Read the bricks-only figure as “what the rest of the set costs me, spread across everything in the box”.
Enter the minifigure count and what you would value each at, and the calculator subtracts that before dividing. The result answers a different and more honest question: what am I paying for the plastic?
What to value a figure at is your call. Look the specific figures up on BrickLink’s price guide rather than using a flat rate, because a common city torso and an exclusive licensed character are not the same thing.