Yeah, the cult always perplexed me, especially the twins and Sentinal, which were said to be experiments performed by the cult using a serum (health serum?). But they are STEM creatures, and unlike all other enemies don't represent anything. Are they memories of experiments in the real world? And if so, does that mean BOW-like mutants exist in TEW? Why?
Also, it was noted the enemies and architecture from that part of the game looked like they were midevil, and a Haunted file said some of them couldn't possibly have been STEM test subjects. Although Kidman was raised in that area and recognised it, so it could be an isolated, primitive cult controlled area. In a newspaper it said mummies were uncovered from the church, so MOBIUS or Rivik could have stolen some, taken their brains, and extracted their contents.
Since Theodore recruited people for STEM, and since Mobius has been around for a while, maybe the cult and MOBIUS are actually the same? Kidman's recruitment, those cemetary experiments and the prevelancy of the cult symbol in STEM could be due to this?
Either way, TEW3 should definately explore the cult, along with their role in both 1 and 2.