There are essentially no hard rules for what a DM does in his own game. We want games to be consistent with the world we've collaboratively created, out of respect for the community, and we generally want to avoid things like world-ending scenarios, but other than that, DMs can do basically whatever they want.
Mind Flayers aren't open material. But if you want to use them in your game, please do! DMs can have any kind of monster, from any material, and have NPCs with levels in classes from any source book. Want to run a published adventure? Go for it! The judges will help you put into the context of our world, and then you can run with it.
In your own game, you, the DM, make the rules. The adventure approval process and the judges are here to help keep the world mostly consistent and mostly balanced, not to stifle creativity and scare away potential DMs.
When I've submitted adventures, I've gotten nothing but positive feedback, and sometimes some inspiration that made my adventures even better. Think of the living world as a springboard for your ideas, rather than a spell of planar binding.
The bureaucracy is incredibly loose, so don't let the proposal deter you. As long as you have some sort of plan for scaling the adventure, we will approve a wide range of levels. Even if you have doubts, send what you have our way, and we'll work out the kinks together.
Gods willing, soon we'll finally get some of those no-good, gambling fools out of the inn and on the road.