It's true that most of the water in the shower will hit in the bottom two or three feet of the walls and on the floor. However, there's a reason that pros will waterproof up to the height of the shower head.
Water vapor will penetrate the grout up much higher than three feet, just not to the degree that it does in the lower half. How sure are you that there is no mold or damage in the upper part of the shower that you intend to leave untouched? If you knew right now that in two or three years you would have to tear out the walls all the way up, would you proceed as you plan to right now?
To answer your questions, though:
1)If you put 6 mil plastic on the studs it needs to extend over the flange.
2) Use silicone to fill the 1/4" gap between the shower base and the Hardibacker
3) Since this is only a 1/4" gap it shouldn't be an issue, unless the tile are very small. However, you shouldn't be using mastic in any shower application. Use thinset mortar that comes in a bag and must be mixed with water.
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The top ten reasons to procrastinate:
1.