The window setbacks should only be taken in account in the zone area calulations when they reach the floor. Otherwise, that space isn't available for use and, therefore, it isn't calculated in the zone areas:
In case if the window reaches the floor, the setback has to be calculated if it's deeper than 130 mm, though:
In the project in question the floor consrtruction, however, consists of two main parts - carrying reinforced consrete slab and the finish floor construction. The tops of the reinforced concrete slabs coincide with the floor levels.
In this situation, when the zones are created automatically, the window setbacks don't get calculated. Is it possible, somehow, to still calculate them, despite such floor level settings?
for some reason zones don't calculate these setbacks for Windows if they are placed like in your screenshot and you have 2 options how to set it, each option following the method of anchoring the window.
1) You can use the the lower tolerance in Nominal sizes and tolerance settings. You have to set the number the height of the floor above the construction slab. But careful for the parameters, you also need to extend the height of the window by the number you have putted in the lower tolerance. Also you need to lower the vertical position of the window.
2) You can use the wall inset. There you need to activate it and again set the height of the floor with minus (eg. -150). Then you also need to tell how much it goes to the window (from inside face to the frame of window).
Both of these options will then calculate the setbacks. I'm attaching pln file, so you can check the settings for yourself.