I am not an aero guy either, but I have been closely following Formula 1 since the late '70's

.
With that proviso, I think you might find that the biggest issue is the gap between the RTT and the trailer, not the overall height of the trailer. I'm pretty sure your trailer is already much shorter than your 4 Runner. My guess is there is quite a bit of turbulance created by funneling airflow between the tent and the trailer lid. If that is the case, you might think about approaches to closing off that gap rather than actually lowering the tent. That would allow you to still keep the solar panel under the tent, and perhaps even some other similarly flat items.
Think about the kind of thing you are seeing semi-trucks do to close off the gap under the trailer.
While I agree with Bob though that any milegage gains are likely to be small, to cost to acheive them may be small as well.
Just a thought.