A reality in which Trixie took over equestria was scripted, but ultimately cut from the final product due to time constraints.
A reality in which Derpy ruled was proposed but was cut as it took away from the tone
Zecora's look in the Chrysalis reality is based on that of Storm from the X-Men comics in which she was in the Savage Lands for a time.
This episode and its predecessor are the first times Queen Chrysalis is addressed by name in the series
Fan favorite character Trixie can be seen standing on a roof with Doctor Whooves during the scene where Chrysalis and her spies infiltrate Zecora's hiding area. This was confirmed by director "Big Jim" Miller.