Here are some of your more interesting considerations:
Above the garage:
This space will be much harder to sound isolate from the remainder of the house.
This is also one of the few, if not the only, space in the house which is over non-conditioned space, below non-conditioned space, and with three walls exposed to the exterior...net out. Space will require considerably more A/C than the basement option.
You can install, and hide, a window, if you plan for it now. Do not even think of using a "pocket door". They rattle big time.
It is not likely you're going to get sand into a stage in this space. The static load of the sand will require rather significant foundation and structural changes. Sand in the stage is a good thing, not a bad thing, if you can do it.
You can "cheat" the ceiling with soffits...been there, done that, and you may find pictures of those who've done exactly that.
Most people, when they entertain, have their entertainment spaces in the basement and main floor avoid guest traffic into what many consider the "private" spaces on the second floor.
You do not want your sub bouncing the floor under your feet. All that means is the sub is using it's abilities to move the house, not move air. If you want some tactile energy...there are better ways that don't involve moving the whole house (or a large portion of it).
The fact that it is a basement does not mean you can skip floor isolation.
Unless you have a comprehensive set of plans for the builder PRIOR to construction of the house, you'll likely find a high level of disregard for clear ceiling spaces. You'll have plumbing and HVAC almost randomly placed below the joists.
The theater walls adjacent to concrete walls still need to be constructed with isolation techniques. Concrete is a wonderful transmitter of sound (as are steel beams).
Due to structural support, you may find steel columns or support posts in places most inconvenient for a clear area for the theater/music space.
Modes in General.
The nice thing about golden ratios is there are so many of them...pick one that will give you the answer you want ... it will be wrong anyway. That being said, in residential spaces you will have modal response regardless of what you do with seating and room dimensions. There are other and far more effective ways of dealing with room modal response issues (and you're going to need to do this in any case). So design the space to fit your functional requirements. BTW, the soft flexible wall thing is a certain amount of non-sense. Your walls become speakers and what is really happening is your walls are more transparent to low frequencies meaning the reduction is bass modal excitement is really as a result of a reduction in low frequency energy in the room. Solution? Bigger subs. Oops, now I have real modal (and other problems).
Modal spreadsheets seldom, if ever, are accurate predictors of room modal response. They fail to take wall impedance and a long list of other factors into account. You may be sweating a dimension to reduce a mode which, when the room is finished, wasn't a problem to begin with.
You would get the same two-channel response from your speakers whether they were hidden or not. With the speakers you have, you'd get a better result from baffle mounting in any case. As well, you need to decide your primary use for the space - two channel or multi-channel (I didn't say music vs movies, btw). The acoustic treatments for each are very much different. You can compromise two-channel, or you can compromise multi-channel, or you can compromise both. Your choice.
You didn't mention which surround speakers you have; but, if they are monopole, plan on keeping your seating distance about 15' from the speakers ... alternatively plan on three pair of sides and one pair of rears.
What did I miss?