That's a great point and something I've forgotten about (i.e. the active members of the cult believe they're following a legit god). That makes more sense to me.
So even if the cult on shore belong to the Mindflayers on the Nautiloid, the cultist won't necessarily know its Mindflayers they're dealing with. It explains why Larian put that scene with the trapped Mindflayer at the crash - I'm blow him up, but it's clearly made out that the Mindflayer can warp what you're seeing in your head, so even if they work with the cults at any capacity they never have to reveal themselves.
This kind of explains for me why we end up where we end up when we activate the transponder - the Cult at the Selune temple is probably a "saved location" since it is one of the cults the mindflayers are building up.
