In chapter 6, when confronted with a talking purple unicorn, Mike manages not to freak out, mentioning that he "learned a long time ago how weird the world can get". This starts making a lot more sense when we learn that this is happening on the same Earth as G.I. Joe and G1 Transformers.
Alternately, this leads credence to the theory that Tirac was the one who corrupted Luna.
Chip can walk now, because he's wearing an exosuit like Jessica Morgan in "The Return of Optimus Prime, Part 1 & 2".
Granny Bonnie, the creator of the world where Ponyland/Equestria is, is named after Bonnie D. Zacherle, the creator of the original toyline that started it all. Faust the Scribe is named after Lauren Faust, who revitalized the franchise with My Little Pony: Friendship is Magic.
In "United We Stand," President Abernathy almost seems to bend over backwards to avoid having to fight Empress Celestia and her forces. Given that he's a former GI Joe, and lived through things like the Decepticons, the Inhumanoids, and more, it makes sense that he's not immediately trying to jump in and fight yet another war.
In The Conversion Bureau: United We Stand, it's revealed that Starscream took a bunch of Decepticons and settled a small planet of their own. He comes to Cybertron to barter the Decepticons' aid to Earth in exchange for a serious peace treaty. Meanwhile, the other faction of Decepticons follows Galvatron, who has gone nuts, his faction has low morale and supplies, and is more of a nuisance at this point than a full threat.