Do the algorithms take square footage into account at all? The reason I ask is I have two zones with mostly identical settings, e.g. Soil type, root depth, precipitation rate however the square footage is vastly different - one zone is 3x the size - Yet it calculates the same time for both.

Is this as designed? If so what is square footage used for?

If the precipitation rate is the same, e.g. the large zone has three times as many heads (of the same type) as the small, and the additional pressure drop is insignificant, then the times should indeed be the same. The large zone is using water three times as fast.

OTOH, if the large zone has the same number of heads, adjusted to cover the larger area, then you should specify a precipitation rate about 1/3 of the small zone’s value. It will water about three times as long.

A given Soil type, root depth and Allowed Depletion determine how much water will be put down each time. The Precipitation Rate determines how long it takes to do that. So yes the times will be identical with zones with those same properties, except of Efficiency and Sun change them, but the change will be small.

Square footage can help determine savings, or you can use it along with water flow to determine your actual Nozzle Inches per Hour. As Nozzle Inches per Hour is just that, total water per hour, if a zone is twice the size it will take twice the water to fill, but not twice the Inches per Hour.