The actual Operation Crossroads was a series of atomic bomb tests at the Bikini Atoll in 1946. A variety of surplus World War Two ships were used as targets to demonstrate the effects of nearby atomic explosions.
Jackson van de Kamp's blog username is @rever: French for "to dream," Portuguese for "to see again."
The blue and white ferry boat called the "Chimera" is actually the "Queen of Sidney" and is awaiting salvage near the town of Mission, British Columbia, Canada. The same ship has been used in other shows, such as The Bad Place (2017) and Wayward Sisters (2018).
A case of "creepypasta" coming to life would be that of the "Slender Man" in the United States, which may or may not be the inspiration for this installment of the X-files. In the case of "Slender Man," two Wisconsin girls try to murder their fellow classmate in order to impress the fictional character so that they might reside in his home in the woods.
The Ghouli character, seems to be pulled from the Internet phenomena known as "creepypasta," in which every user offers a slight variation of an "urban legend."