What if Apeiron wouldn't have gotten Weaponsmith (Light of Terra DLC 5 A Sky Filled With Steel - Warhammer 40,000) 300 during Dragon's Interlude.
Then would they have gotten his ID and a raid shortly thereafter but without any tinker workshop to confiscate. Joe himself would also have left.
Dragon wouldn't have gotten Joe's ID (where from? I doubt he used a single IP, much less a fixed one tied to his ID), she would have gotten his geographic location only.
Dragon outhacking Joe on his home field would have been futile (unfamiliar OS, unfamiliar hardware, joe had hardware access, e t c), so she wouldn't have gotten into his system. If duplicate had enough time to get a link to the Laboratorium, duplicate could have simply shut down external connection in even less time. At most Dragon would have gotten access to GSM/CDMA stations and triangulated Joe's location from there. Location would have been +-10m at best due to multiple walls and metallic structures around (also depends onto location of Joe's receiver, if it's in the workshop it would have muddied the water further). If Joe used 'hacked' routers, that might help narrowing position down a bit, but not by much.
Dragon could have potentially matched signal strength of nearby phones with workshop's one, to figure out if there are any phones in the workshop. But that has own issues: multiple phones would have been nearby and such match won't mean much overall: phone could have simply been inside a lift, near something metallic, a fluke due to gsm-based way of geopositioning being unprecise by nature, e t c. Match wouldn't have been sufficiently conclusive.
Even with precise location and a raid minutes after, which is very doubtful, local PRT is not that fast at their best, much less for raiding a populated house that likely needs to be cordoned first, Joe could have easily crafter a decoy relay (or several), placed it somewhere in the building, then let PRT find it. PRT would not find his workshop by definition and later will assume that the workshop wasn't there at all: where and how would a fresh tinker build and power a workshop, silently! in a populated residence? They might suspect a pocket dimension, but I doubt that those are mobile, and tinker would have picked a place where it's easy to deploy and receive a vehicle discretely, a workshop in an apartment complex is just silly. A relay however totally makes sense - multiple residents have own phones and routers so it's simpler to get higher bandwidth and mask higher network activity of the relay.
Another option (does not exclude previous one) is to go back online from somewhere else. If he moves his workshop couple kilometers away (will take him minutes), and makes it clear that second attempt was still from a workshop (ex: place workshop somewhere with a better network, add something new) it will be immediately 'obvious' that a relay was used at previous location. Even if Joe loses again, he will leave PRT non the wiser about his location.
One more option was to remotely reboot GSM/CDMA stations in Joe's vicinity before dragon got to them, with a command that will also wipe logs on startup (it's illegal to tamper with those stations, but he already did either way). At most dragon would have gotten a very vague area of Joe's location, may be a rough area of his house if routers were used and rebooted as well. Still enough time to plant decoy-relays somewhere. It might result in some area-monitoring by Dragon, but as long as there were no other oddities in the area, Joe would have been fine.
Joe was very pessimistic with his assessment, he had multiple options even if they weren't a victory. Weaponsmith was just the most convenient that permitted him a victory.
Edit:
With Joe's crafting time he also could have made a relay, tied it to a drone and sent out of the window/roof, switched to using relay instead of a direct connection.