Notice that the 2GR-FSE does about 65 kw per liter in specific horsepower output but the FA20 does about 75 kw per liter if you do the math. So this engine has already improved on the previous D-4S system significantly in that area.
Long duration with high lift (they tend to go together) is bad for fuel economy during normal cruising conditions in part due to fuel atomization issues. Look at the lift & duration profile range on the Nissan VVEL (VQ37) system:
You can see that the VVEL system is capable of being very mild or very aggressive depending on engine conditions. This allows good specific output and good specific fuel consumption. I'm sure Toyota could have put their system on the FA20 but it just came down to costs. Maybe in a mid-cycle refresh we will see it on the BRZ/FR-S.