Take a standard base framed cabinet 30 inches wide into custom layout.
Take that cabinet into cabinet editor and add a 1/16 inch scribe to the left stile and a 1/4 inch scribe to the right stile. Return to room
Select the standard upper framed cabinet and change the size to say 40 inches place it over the base cabinet.
Change the scribes on this cabinet to the same as the base cabinet
In the elevation view click on the base and upper cabinet and do a resize/equalize on them select the base cabinet as the anchor and select equalize.
The upper cabinet is resized to 29 11/16. Smaller than the base by the combined scribe.