I think this will help explain the width of doors and windows.

This is a default door set at 3' wide.



Here's that box set at 3' wide in front of the door.



The width and height includes the frame of the door and/or window.
Does that help?

Increasing floor thickness would add to the bottom of the floor, not the top. Hence adding thickness to a floor will not raise furniture sitting on it, nor will it raise the walls.
The point of setting the thickness of a floor would become apparent when you create a second level/story or a level set at sub-level, like a basement.
You would have to allow for the thickness of the floor when creating other levels.

I guess my previous door dimensions should have read 3' width, 11 5/8" depth, and 7' height.
There is no length.