A port is air, not air and the walls that surround it. That is called the port structure, and a port length calculator has no need to know how thick those walls are going to be. The calculator's concern is the dimensions of the port air.
"Port width" and "port height" are the specific dimensions of the port airspace that you will input into the calculator. You also will input the air volume of the box you are planning, and the intended tuning frequency.
When the calculator gives you an answer for port length, that is the length of the air in the port structure. It is up to you to figure out how to contain that port air and build it within the box structure. You will be building the box large enough so that it still has the volume that you inputted but also enough additional space for the calculated port and the port structure.
Be sure you are attempting to use the correct calculator, titled "slot port length calculator". By what you said, it seems you may be looking at the volume calculator directly below it. https://www.the12volt.com/caraudio/boxcalcs.asp#porsq
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Build the box so that it performs well in the worst case scenario and, in return, it will reward you at all times.