I would say that most of the wisdom in Trajectory of Fear (https://nerdsonearth.com/wp-content/uploads/2020/03/Trajectory-of-Fear.pdf) would work here as well even though it's about Horror.
If you think about the steps presented there as of Unease, Suspicion, Anticipation and Revelation then the advice should work really well.
"I can’t really do the same with my homebrew world which has very little in common with the real world." I don't think that is necessarily true but it requires the players to have a proper understanding of what is normal and expected.
I would say that many Mind Flayer villains are quite interesting because they are Mind Flayers.
Alexandrian had some interesting thoughts about what to avoid when running rival party in his Call of the Netherdeep -review (includes spoilers about the adventure): https://thealexandrian.net/wordpress/48216/roleplaying-games/review-call-of-the-netherdeep