How the number is worked out
The area is divided by the area one tile occupies - and that is the tile face plus the grout joint on two of its sides, not the face alone. A 12 x 24 in tile with a 1/8 in joint covers slightly more floor than its nominal size, and ignoring that over-orders by a few percent on every small format.
The cutting allowance is added to the area before the division, then the tile count rounds up, then the box count rounds up again. Two roundings in the same direction is deliberate: the failure mode being avoided is a half-finished floor and a discontinued batch.
Layout decides the waste, not the room
A straight lay wastes offcuts only at two edges. A diagonal wastes a triangle at every perimeter tile, and herringbone wastes one at every angled cut in the field as well. That is the whole reason the pattern is an input here rather than a footnote.
Adhesive and grout
Not included, deliberately. Both depend on the notch size of the trowel and the flatness of the substrate, which vary more between two tilers in the same room than between two products. That calculator is on the roadmap as its own page, where the assumptions can be stated properly instead of buried.