Weird situation at the extraction from almost every Mission

So we are send in to most of the Missions to cleanse, clean or restart places and machinery.
Yet at almost every Mission of that kind, we are getting chased on our way to the ship or the elevator.
Many of those Chaises are having an ENDLESS horde spawn.

Shouldn’t we leave those facilities CLEANSED?
The extraction ship should only land after every single heretic in that last area is killed. Same goes for elevator doors, that should only open, after the area is purged from heretics.

Every extract should be like Enclavum Baross or at least like Consignment Yard HL-17-36 with enforcement troops going in, after the strike team dealt with the real threat.

I think that the “cleansing missions” like forge, water facility, and the others are just us the player cleansing the demonic corruption. We don’t take the facilities since they are so robust they can’t just be destroyed by the cultists (or corrupted again without major effort). It’s pretty believable to me in a 40k hive city context.