To elaborate: Most of the fic's World Building is on the forums, in the form of "extra documents" written In-Universe (for instance, Cloudsdale is described in a tourist brochure). There's also some elaboration of story elements in the discussion. None of this is necessary to understand the fic, but definitely helps flesh out the story.
Androids Are People, Too: In the Trade Order, AI's are considered legal citizens, and are usually treated with as much respect as those of flesh and blood.
And I Must Scream: Word of God on what happened to Discord. The Traders sealed his statue in a small ship, put it on auto pilot towards empty space, and kicked on the FTL. A ship can only drop out of FTL if it enters a strong gravity well, and their are very few planets or stars in the ship's path. And Discord is still stuck as a statue during all of this.
To make matters even worse for the bastard, the overall flight path is perpendicular to the plane of the galaxy, so he's heading straight into intergalactic space, the emptiest place in existence. There won't be any conflict to free him for a long time.
Also what happened to some members of the Horizon Corporation, also by Word of God. While the Universal Trade Sanction (which makes them unable to even buy food) was handed down by the Investigation Directorate, the various factions of the TEC also handed down their own punishments...including Cognizant Cryocontainment.
Genetic Engineering: Deconstructed with Twilight Sparkle. It is implied that she is genuinely dangerous with her mental block restricting most of her potential disabled, and a great deal of her personality is based around this fact of her life.
Mega Corp.: The TEC is an alliance of these; Rarity's ship is even owned by one.
Noodle Incident: Apparently, Fluttershy joined Rarity's crew in some rather over-the-top antics on their last shore leave.
And Colonel Rekav is no longer allowed to gamble anything, for some reason.
Sci-Fi Writers Have No Sense of Scale: Averted. The author goes out of his way to make it clear that space is fuckinghuge. He even describes Twilight and Spike seeing the TDN Novus as a tiny point in the distance as a minor miracle.
Dalek Ix, after doing a rundown of how distant things are in space: ...And I'm not even going outside the solar system, which on cosmological terms is roughly equivalent to one's house. No wonder SoaSE ships go into FTL for in-system travel.
Shout-Out: Several, mostly to Battlestar Galactica, such as Rainbow Dash's callsign (Starbuck), the Everfree Forest Cloudbase, which superficially resembles a squared off Cylon Basestar, and the use of the word "frak".
Equestria's Argonev starbase is called the Kasztanka.
The Stinger: Both chapters so far end with flashbacks to Twilight's past, in the form of "holo-vids". Word of God is that Celestia is the one watching them.
Super Soldier: Twilight was intended to be this. Her rescuers had other ideas.
The High Queen: Princess Celestia, who is still ruling Equestria, controls most of the pony species by the strength of tradition and by being an honestly good ruler and noted as being one of the most important members of the TEC.
There Is No Kill Like Overkill: How the Traders dealt with the Horizon Corporation. Along with their lab (and the asteroid it was on) being blown to smithereens, the entire organization was essentially erased: all of Horizon's money and resources were seized, and everyone who worked for them was either killed or arrested. Moreover, the Traders were completely banned from doing business with Horizon's employees, via the Universal Trade Sanction—the bastards can't even buy food. And that's not all: the UTC was handed down by the Traders as a whole, so the various members also laid down their own punishments in addition to all of the above. Literally nothing is left of Horizon by the time the story starts.