But they might have reduced the number of stamped parts by an order of magnitude, improved wiring in a revolutionary way (there’s a patent by Tesla for that), MUCH less R&D and production setup than model 3 (they won’t make all the mistakes twice),... and let’s not forget economies of scale, they will produce more Y than 3.
All of this is theoretical and we don't have any real data on how it will affect gross margins. When the car is larger, many things are going to be more costly, like painting, which takes up a significant part of automotive margins.