I don't make foundry missions, but you could build your set up in the air and use false floors, (hinged), to make bodies disappear when the lights are off. You could also use a false, (hinged), ceiling to make them appear, again when the lights are off. I saw a video on YouTube about this but I'll be damned if I can find it again.
Using custom sets built high is the only way to get rid of NPCs. Removing the floor under neath them and then replacing it a second later with another bit of flooring is the only way.
It won't really work with scenario 1. in part because we yet dont have movement paths for NPCs but also because the player will see it.
For 2 you will need to work out triggers. That is what will trigger lights going on and off. In this case I recommend reach markers but be aware you need to make sure they will be hit in sequence.or otherwise a light will be left on and it will ruin the effect.
The player surrounded by bodies and enemies would almost be impossible to do as to get rid of them yo will need to remove the flooring which will probably include the player. Though yo may set up an invisible wall in a single bracket sort of shape to funnel the plaer to a point which has additional small object that will prevent the player falling when you remove the flooring. Though that will only work for stuff in front of them not behind.