I think the biggest challenge with having the tent that high up will be accessing it to unzip the cover, release the straps, tuck in all the excess material when folding, etc. Mine is mounted on a bed rack and I stand up on the rear tires and sides of the bed to open and close the tent. You'll probably have to carry a small step ladder in the truck to get up high enough.
You can mount it so the annex opens backwards. The mounting rails are normally configured to open over the side, so you'll have to change their orientation when you first get the tent. Not a big deal. The Annex has to be taken on and off each time you fold the tent by sliding it through a channel along the hinge line of the tent base. Takes a little time and is harder when it is way over your head.
The other issue I see is interference with the tailgate and hatch on the canopy. The annex wants to hang straight down from the hinge line on the tent so it'll be laying against the truck. Not sure about other tents, but in our CVT the "door" on that side of the Annex is really just a zipper flap (no bug netting) which is smaller than the wall of the Annex. I don't think that it would allow you to open the tailgate and the canopy hatch to access the truck bed without stretching /bulging the Annex in some really weird directions. I would certainly want to try (rent a tent or test fit) before you buy to ensure it'll work the way you want.
Awnings on the side should be no problem, they usually attach to the bars of the roof rack so as long as your tent isn't hanging out over the sides it shouldn't interfere. The height may be an issue for set up and pack up, same as you have with the tent.
I don't see why you wouldn't be able to put an additional rack over the truck cab. They'd be different heights but still functional for carrying cargo. There are several examples on here of trucks with both cab and canopy cargo racks.
I don't have any data on the MPG loss. I would GUESS in the range of 5+, but I think it would depend a lot on how big of a truck you've got and how much / how fast highway driving you're doing. It would probably be closer to 10 MPG on my little Tacoma.