1) With beato's red line about "
この六軒島には１９人以上の人間は存在しない", I actually can't think of it as a "proof" that the dead doesn't count. The biggest issue is that Beato confirms the first 6 "status", using again "
人" which shows that Beato still claims they are "human", despite "dead" so they count in 18. Also, if we take into consideration Eva-beatrice, well
2) I'm quite not convinced about the "natural death" portion. The natural death wouldn't exactly explain how and why everyone got in a gigantic 6 cell closed room.
Though I will agree that the weak point seems to be the windows in such case.
Still about the sanctuary, I believe we can rule out the fact it is suspicious they didn't start by that: whatever there is a corpse in the boiler room (stench here), they wouldn't exactly expect the sanctuary, especially they do have that automatic reflexe due their childhood not to approach the holy sanctuary so heh.
3) I still have doubt about Gohda's "innocence". The biggest problem in episode 2 is that natsuhi's room is closed from the inside, there isn't any key aside the one in the room, and all the master keys are under rosa's custody so humm...