Your diagram shows a pathway around the riser that is close to the wall. Make sure that you have sufficient width and ceiling height so that you don't bump your head on the sloped ceiling as you walk there, especially in the dark.
1: Graph paper is your friend. Although there are online calculators, I find it easiest just to take some measurements, draw it out to scale on the graph paper and use a straightedge to visualize the sight lines.
2: If the top layer of your riser is not thick enough, it will vibrate like a drum head and sound as well as feel hollow when you walk on it. Green glue between layers is great if you have some left over, but roofing felt also works. Filling the space with fluffy insulation helps eliminate resonances. The bigger that you can make the vents on top, the more it will work like a bass trap.
3: I like that idea of putting the subs behind the knee walls. I generally avoid placing subs pointing up for several reasons. Unless you put some sort of cover on it, objects might fall on or get placed on the speaker, causing damage. Dust and small objects can fall on the speaker and stay there, causing rattles and buzzing. Dust won't be a huge problem, anything like the size of a grain of sand or bigger might.
4: It certainly can't hurt. While the other walls will allow flanking paths to the rest of the house that can be unpredictable, the back wall is in a position to be a direct sound radiation path. The cost of the extra drywall and Green Glue for such a small wall would be so minimal that you might as well give it a shot.
EDIT: Others may disagree, but thinking about this further, I'd actually be inclined to build the back wall as a double stud wall with two layers of drywall and Green Glue on the theater side. Certainly some of the benefit will be "short circuited" by flanking through other walls, but given that this wall is in common with the rest of the house, it would act like a drum head to transmit sounds to the other side. Partially decoupling it could offer improvement for a very minimal cost. The extra cost of some studs would be in inconsequential and the labor is minimal. If you build it with 2x3s instead of 2x4s it will minimize the wall thickness. You can make good 2x3 substitutes by ripping 2x6s down the middle. They will be slightly thinner than normal 2x3s, but the difference won't matter. You can usually find good, straight 2x6s to work with.