Not quite. The druid's thousand faces ability only allows you to gain the benefits
while in your normal form. Which means that Alter Self layering only works if Alter Self is the lowest level of the transformation.
What does that mean? It means that you transform into a Dwarf and an elf before you wildshape into anything, because that gives you extra weapon and armor proficiencies.
1. Just how exactly do the mechanics for "layering" Alter Self, Wildshape, & the Shapechange spell work regarding sequence of activation?
Your "form" is that of the most recent transformation. Every ability granted by every previous level of form changing is still in effect unless a subsequent round of form changing would remove it. Note that the list of abilities you
get and the list of abilities you
keep are totally different, and can be massively exploited (note that weapon proficiencies always accumulate, while vision always goes away for some reason).
The Druid Alter Self can only be turned on when you are in your normal form, but it stays on after you transform into another form (for example, by the change enacted by the ability itself). Shapechange can trigger a new form at any time the spell is active as a free action. Unlike other form changing, it replaces itself. This means that if you shapechange into a Fire Giant (gaining heavy armor proficiency for some reason), and then take a free action to transform into an iron golem, you lose the heavy armor proficiency. OTOH, if you shapechange into a Fire Giant, and then polymorph any object into an iron golem, you keep the heavy armor proficiency.
2. If this is all legal (which I believe you, Frank), what kind of insane cheese can you work with this layering effect, from a combinatorial standpoint and using Skip's recent Polymorph musings at the WotC web-site?
Weapon and armor proficiencies stack. Spell-based bonuses stack. You can gain all the benefits of the "animal buffs" (Nature's Favor and such), while having all the armor and weapon proficiencies out of Alter Self, while shapechanged into an entirely separate combat form such as an Iron Golem.
Iron Golem + resizing Dragonhide Magical Armor + Magical resizing Dwarven Waraxe + Magical resizing Darkwood Shield is completely hillarious. And by hillarious I mean that your armor class is in the sixties and your attack bonus is high enough to hit yourself.
3. Does all this layering get kiboshed when a Druid wildshapes into a Plant (at 12th level) and tries to use A Thousand Faces? Or does the ability to wildshape into a freakin' bi-pedal Vine Horror *and then* layer Alter Self/Changeshape remain legal and therefore somehow abuseable?
You have to put up the Alter Self first, so the only thing you can hand up to the plant form is continuing spell effects or abilties that the Plant form doesn't get rid of.
So you could, for example, Alter Self yourself into a Dark Creeper to pick up some sneak attack and weapon proficiency, and then Wildshape yourself into an animal and then cast Nature's Favor and/or Nature's Avatar on yourself, and then Plant Wildshape into a Vine Horror.
That would work.
But you can't Plant Wildshape yourself into something and then Alter Self yourself into something else with the thousand faces ability because it only works in your normal form.