But the width of the box is less, so the area is the same. E=1/2 Mv^2 - it doesn't matter from a pure energy standpoint how fast or slow you get there.
Thats true, but a bit misleading in context. You're correct that the energy use for the acceleration events is basically the same, but the slower accelerating car will use less energy over equal timespans, which is how most people (I believe) are considering this scenerio with respect to hypermiling. If a fast car accelerates to speed in 10 seconds and a slow car does it in 20, the fast car uses more enery at the 20 second mark since its average speed over that 20 seconds is higher.
That higher average speed also contributes to more aerodynamic losses over the same period of time and as you point out the electrical losses from the faster acceleration are also higher. That all adds up into what most people will intuitively suspect, which is that you use less juice driving with a light foot.