G.I.R.L.: Monica Gilbey-Bieber's real name is James, which is also Plankton's second name. This leads to the possibility that Plankton is the real self-insert and not C'ren. Aside from that, Jimmy also stated that he is quite short, just like Plankton in canon and in the fanfic.
Meaningful Name: Monica Gilbey-Bieber, as a penname, is an alteration of moniker and Gilesbie. Bieber is self-explanatory.
Obfuscating Stupidity: Word of God declares this as his reason for trolling. He pretended to be an idiotic, Preppy Valley Girl and see how long he can last. He only survived for 27 chapters out of the planned 69 until he eventually broke down and confessed several months after a sudden hiatus.
What Could Have Been: There is a long explanation of these in Chapter 13 of the author's commentary. This will explain a lot of things in the story, such as how C'ren can breathe underwater and how Justin Bieber discovered Atlantis. He did say that there were no sex scenes being planned at all, but he later contradicts this in Chapter 15, where he wrote a preview of a sex scene between C'ren and Justin Bieber in the commentary with text the same color as the background just like spoiler marks here in TV Tropes.
Word of God: The author has a commentary of this fanfic in his blog.