Small protrusions are definitely not a concern, anything sticking up is within the boundary layer. Something to keep in mind with vehicle aerodynamics, you're manipulating air out to 3-4 feet from your truck and more, often times people have it in their head that we're only worried about 6 inches to a foot of air. The shape of your vehicle is key to good aerodynamics, texture does little to nothing. We'd all have golfball dimpled cars if it did.
Your intuition about power and MPG betrays you. If you put a 120HP Honda engine in a Corvette, it would get 38MPG, or better. Look into BSFC charts for the detailed reasoning behind this, but basically, an engine uses fuel more efficiently when it is running at 70% of its rated HP. It makes the most power for the fuel it is using. Here is a good AutoSpeed article that talks about this.
BSFC Explained in AutoSpeed
If you want to improve economy, you'll figure out a way to suck warm air into your engine off the exhaust manifold or something. I must admit, this is not a forte of mine, I understand it a bit, but the practical application of warm suck air, I know very little about. Look for WAI in ecomodder, and there are plenty of folks who can give you better nuts & bolts advice.
If you buy a big sheet of aluminum, you may want to consider using some lumber as a frame underneath it. You could cut a very precise shape out of the wood. I know when redwood dries, it is crazy light and it is rot resistant. I'd think 2x6's would give you 4 stringers fore & aft to build it. For something as low profile as what you're looking to do, I don't think the sides would make much of a difference. But radius edges would IMO look better and perform a little better in cross wind situations. Fabricating them would be a challenge no doubt.
Something else for the plus column on your idea here, you'll have a double roof on your truck and cap, this will make it more livable in extreme temperatures and possibly quiet the ride some.
Hope this helps.