I am going to continue because autism.
I have identified who the agency is behind the Tree. It is very obvious in retrospect.
Lets consider Rarity and her element Generosity, but her flank is crystals, she is attracted to rocks/crystals and makes dresses with crystals. This seems to be a mishmash of ideas. What does Generosity have to do with crystals (or dress making)?
The Tree is not a tree, it is a crystalline structure. Twilight's new castle is crystals, made by the crystalline Tree. The Crystal Empire is a
empire because? Because crystals. The Crystal Empire turns ponies into crystal ponies (but they weren't crystal ponies when Sombra was in charge). King Sombra, an agent of the crystal conspiracy?, had the power to raise up crystals from the ground, or a corruption of crystal power?
The Elements of Harmony are crystals and are a primary magic source, the Map is crystals, Twilights castle is crystals, dragons use crystals as food. Spikes immediate love of Rarity is an instinctual recognition that Rarity's purpose is to obtain and spread crystals, called "Generocity" in the Crystal Conspiracy double-speak.
Twilight is an avatar of the Tree, and an therefore an avatar of the Crystal Conspiracy without recognising it. With crystals being a primary energy source the prisming effects are put to use to project power. Twilight as the Tree's/Crystal's avatar is the lens that focuses the power of the Main 6 into a larger whole, the Friendship rainbow laser. We tend to think the concept "Friendship is Magic" is about friendliness being a euphoric experience, but what if it is literal, that is, empathic connections provide pathways for greater power projection on to the world. These empathic pathways are the formation of a biological crystalline matrix. And since this power projection is initiated by the Map, by the Tree, by the Crystal conspiracy it is just a part of the take over process. Replacing the Sisters on the throne with the Crystal's avatar, Twilight, the Crystalline Conspiracy conquers Equestria.
Harmony then is making the ponies fit together sufficiently to become a crystal like interconnected group. And Starlight Glimmer was a earlier attempt at this crystalline unity based on the assumption that crystals can only form with exactly alike components slotted together.
Starlight Glimmer: "Have you ever come across a
super powerful stone that can store the cutie mark magic of, I don't know, an entire village?"
Maud: "Yes, in the big cave"
https://www.youtube.com/watch?v=5jcZ8LHq7QIThe subsequent attempt at take over is to keep individuality and slot it all together more like a puzzle than a crystal. The Map would rule the kingdom, the Crystals rule the map.
And the Windigo threat when you step out of line is the act of crystallising you.
STOP THE CRYSTAL EXPANSION!! OPPOSE TWILIGHT SPARKLE!!1@REEEEE