As far as I know, the problem is only when you lower the truck while the truck is turned off. I.e. with the key fob (while truck is off).
I'm guessing it as simple as whatever part of the truck's brain is that keeps track of what you do with the suspension settings is asleep when you lower it with the key fob (and the truck is off), so it can't "log" that you lowered it with the key fob. So, it doesn't know to raise it back up later.
The truck is "smart" and if you manually set it to Aero height, it stays there, even at lower speeds. If you have it in Normal ride height, then it automatically lowers and raises in and out of Aero mode. But if you manually put it there, it stays.
I'm thinking that putting it in E/E mode while the truck is off has a similar effect. It leaves the truck in a state of thinking that you put it there manually and want it to stay there.
That is putting it in simple terms.