For me the military spawned at the elevator as soon as I entered the Cordon, but only if I went immediately when told to follow the guide to Cordon. I paralleled the road to avoid the radiation and almost missed the bus stop fight, it started so quickly.
And I totally agree about game-stopping scripting failure - I have 54 hours in the game per Steam and I'm maybe five hours max into the game. Now I have to go back into the Swamp to get the good detector, sniper rifle, and artifacts, plus some upgrades, and I'm worried what else may break if I don't go straight to Garbage.
I just loaded my pre-Cordon save and went there. Entered by the military base. Went into the village. No dots. Walked to the bus stop. No dots.
Went back to Sid and checked for dots periodically. Exited the initial conversation with Sid at every point, and traded with him. No dots.
When I clicked on "Deal" both the military and Loner dots spawned at the bus stop.
Anyway, I haven't talked to Valerian since taking out the military at elevator/garage, though he called me back.
BTW, none of the loners survived those battles, so you don't have keep them alive to succeed.
Think I can play as desired until I trigger the next main mission step via conversation with Valerian.
So I have a save before that conversation in case it goes wrong, but I'll probably just talk to him, as I'm past the major "bug."
Shame the game didn't handle this better.