custom food

No, just enter 'total carbs' like it is on a food label.  That 'carbohydrate by difference' refers to the analytical method used:

"Carbohydrate calculation assumptions
Because the analysis of total dietary fiber, total sugars, and starch are performed separately, the sum of these carbohydrate fractions may not add up to the main carbohydrate-by-difference value."

Perhaps that needs to be eliminated to reduce confusion.

Example:
On a milk label, for a serving, Total Carbs is 12g, Fiber is 0g and Sugar is 11g.  Technically fiber and sugar should add up to 12g, but due to the analytical methods used in the lab, they don't.

My understanding is that 'total carbohydrates by difference' is the total carbohydrates in the food. The "by difference" refers to the method of measuring them, by subtracting measured weights of water, fats, protein, etc and seeing what is left.

The other measurement is "By availabilty" which is mostly the same, subtracting the dietary fiber.

Someone feel free to correct me if I'm wrong.

Oh, you beat me to it. :-)