I have no issues with this.
For me, all Chosen (in their respective strongholds) spawn when one of my soldiers is near the sarcophagus; around the halfway point. I don't think the two enemies inside the room have no connection to whether the Chosen appears or not.
Alternatively, are you using a mod that may or may not be in conflict?
No mods for me. Running on a clean install.
This is so frustrating.
I just played through that part of the game where you fight the Hunter and I had no problems. What you may be experiencing is a bug as you said that does not always happen. I would suggest you contact either Firaxis or 2K.