Actually I see the main lair stacks move on their own anyway, it just takes quite a few turns. (I noticed this when I was waiting for all the monster to move off of their lairs on a wildland so I can clear it.)

I also notice with this most recent iteration that unit stack icons are grayed out slightly.

Yep, and it's still a rather crippling bug because you cannot clear out the Vetrar quest and wildland area if you kill Vetrar outside the area.  Although you get the sword and city item bonus, the quest doesn't complete.  Derek, this really does need a fix.

N/A

I noticed in a recent game that the Obsidian Golem guardians of the Imperium ruins wildlands area immediately started wandering all over the map at the beginning of the game.  This obviously makes it very difficult to clear Imperium as you need to hunt them down.

The imperium always has the settle tile. Sometimes the AI will settle two closely to make this tile visible at times, but it is there from the beginning of the game.

If there is a city too close, you don't have the settle tile.  I don't think there is any requirement to kill all the armies and/or clear all the lairs in Imperium to settle the tile, although you have to get most of them in order to get a pioneer through.  I think you must have an AI city that is too close to the normal settle spot.