While you cannot deal with Destroyers in-person, as they are problem-solving guard dogs, it is extremely possible to go over them and speak with the spirit in charge of the immediate sector, since anywhere that has Destroyers defending it is typically important enough to have an overseeing subprocess. The Quarantine Layer is by no means one unified structure, no more than your lungs are a big pair of air-sacs. So staking out one particular mountain-sized filter-valve or something to repurpose for the task, and defining the undertaking to the spirit in charge of that area in such a way that it does not interrupt its activities, and may in fact actively benefit it by optimizing the local space (such as by crewing the area with mortals capable of defending it without a Destroyer detail), would be the best "diplomatic" direction to address it from.
Just like in Creation, the further you can go over someones head, the more likely you are to find someone who has the authority to do what you want, and stave off the things you don't, but they're going to have demands of their own roughly as involved as accomplishing it yourself, just with less blood on your hands.
Another method would be the Brute Force way, of simply setting up a network of custodian-repelling wards around the designated area, and carving out a section of the place from supernatural dominion manually. This will have a knock-on effect for systems nearby, as now those custodians will need to redirect their patrol routes Around the area, and may not be willing or able to manage the regular maintenance/retrofits, and leaving it to fall entirely under mortal stewardship, on top of the work needed to keep Xexas survivable. This is probably one of the few ways to establish a foothold for a "portal" or Elsewhere conveyance of some kind, because such a huge installation is going to have power needs involving tapping into the nearby geomancy circuits, which is a suitably hard "for your own good" sell to any spirit keen on upholding its domain to peak efficiency.
This may or may not result in a message or possible visit from such a creature, looking to see what is going on and why a significant portion of its allotted resources are being rerouted without its permission.
Thanks again. I had forgotten to conceptualize Quarantine Layer and Pole of Smoke as the Bio-mechanical organ systems they are. Aditionaly, looking for overseers to negotiate with never crossed my mind.