The church of the Flying Spaghetti Monster is just more subliminal programming for when the faked 'alien invasion' occurs.
The 'alien invasion' will either kick off the start of a new religion (a 'church of flying spaghetti monster') or show the destruction of this decoy 'beast from the sea' (a fake 'beast from the sea' convinces people that 'Jesus has returned' and destroyed the 'evil church').
same as Hedorah/ Smog monster from Godzilla
same as Cthulu
same as Brainiac's Skull Ship (villain of Superman). Brainiac would reference a 'time - traveling artificial intelligence/ Singularity 'god'