I think the window frames are set in butyl putty - not a spacer. I have read about gaps in the putty due to bad installation, and water could leak thru the gap.
The pic below shows the most common sources of these leaks that I have noticed by reading the forum.
Of course the window frame perimeter should be caulked/re-caulked from time to time with ProFlex clear (especially across the top and down the side a bit), but also check the bottom trim angle. The roof membrane trim is a possibility for leaks, but less likely than the window or the bottom trim angle.
The youtube video below does not address your specific question about windows - but it is very good for showing common leak points in a slide and how the technician addressed the leaks (and replaced the rotten floor).