Kadeton

There's nothing restricting you to choose only units that are deployed. The rule only mentions deployment as part of the timing for declaring the ability.
You can choose any units in your opponent's army, regardless of whether they're on the battlefield.

Yeah, I'd say Flying High doesn't count as a move, and you can't disembark after it even in an Iron Sky Attack Squadron.
The bit that convinced me of this is the difference in wording between the Flying Transport rule (emphasis mine):
Units cannot join or leave this model’s garrison if it has made a move or flown high in the same phase (they can join or leave before it does so).
And the Bold Privateers rule:
ARKANAUT COMPANY units from this battalion can leave an ARKANAUT FRIGATE from the same battalion either before or after it has moved.
Flying Transport makes a clear distinction between moving and flying high. Bold Privateers only mentions moving, so we have to assume it does not apply after flying high.

You've got the sequencing a bit off, I believe. Scaly Skin reduces the number of wounds allocated to the unit from each wounding hit by 1, to a minimum of 1. This happens after saves, during wound allocation.
So in your first two examples, Scaly Skin does nothing. Your opponent rolls their attack and wound rolls as normal, you roll your saves as normal, and each failed save means 1 wound is allocated to the unit. Since the attacks only deal 1 damage, Scaly Skin doesn't help.
In your last example, Scaly Skin is awesome. Your opponent rolls their attack and wound rolls as normal, you roll your saves as normal. Normally, each failed save would mean 3 wounds were allocated to the unit, but because of Scaly Skin, that's reduced by one - each failed save means only 2 wounds are allocated.
Effectively, think of it as reducing the damage characteristic of every attacking weapon by 1, to a minimum of 1. Then just do everything (hits, wounds, saves) as you normally would.

I'd see the garrison rules as in addition to, not a replacement for, any normal restrictions on where you can place your units.
AoS doesn't have a "deployment zone", there's simply no such thing for them to reference. All you have is a territory, and additional restrictions per the battleplan, e.g. "Units must be set up wholly within their own territory, more than 12" from enemy territory."
So I would assume that the allowance to "set up as a garrison at the start of a battle if the terrain is wholly within the unit's territory" doesn't preclude you from also have to adhere to any other restrictions, such as having to be more than 12" from enemy territory. You're still only allowed to deploy where you're instructed to, but if there's a garrison within that area you can put units into it. The rule is basically just saying that you don't have to deploy on the board and then move into the garrison.
(This is simply opinion, there are no rules or designer's commentary that gives a more explicit ruling on this as far as I can tell.)

Yes, Favoured Poxes does not end during the caster's next Hero Phase. The tradeoff is that your wizard basically can't do anything.