When you use the desktop calculator, the sensitivity is calculated based on the Windows settings.
So in Windows:
1280x720 and 500 DPI = 2.56 inches to move the mouse from edge to edge (1280/500)
1920x1080 and 500 DPI = 3.84 inches to move the mouse from edge to edge (1920/500)
When you convert these two inputs to 1280x720 @500 DPI in CS:GO, you will get different results since the input distance is different.
Makes sense?
Also, it's the game resolution that is important, regardless of windowed or fullscreen.