I registered an account here just to make sure this topic stays bumped and updated, I want an answer to this too! lol
Your experiences are similar to my own emke. When I first played through this mission I thought an "alarm" would be signified with some kind of actual alarm siren going off (there is an audible alarm in mission 3 if you get caught while blowing up supplies, so I thought this mission would be similar) As you know, nothing like this happens.
From having played the mission on 4 occasions with a variety of approaches without getting the achievement, I decided to take notes about where the enemies spawned and how I engaged them. I broke the mission down into 3 phases or "triggers" if you want to call it that.
Phase 1: As you described this is the village approach with reaching blue hat (or warlock in the briefing description) as the primary obj. In the village there are precisely 6 soldiers, 1 pickup truck /w turret (never appears to be manned) they can be easily picked off without alerting each other.
Phase 2: Begins with a cut-scene after reaching Blue hat and seeing exactly 4 Viper members appear. They consist of 2 snipers and 2 rifleman. Sniper 1 appears towards the west of the blue hat building and continues moving north east to the edge of a forested area directly north of the village. If you exit the Blue hat building to the west side of the village while he is moving he will engage immediately. Sniper 2 appears appears roughly 50m east of the village and posts up near a barn beside the road. Both rifleman start moving through a field directly to the front of Sniper 2. If there are any Syndikat remaining (or if you simply chose to stealth your way to blue hat) they will go on alert and start engaging targets. What's most important about this phase is a red flare which is fired after the appearance of Viper team, regardless of whether the Syndikat have been left dead or alive. In all four attempts, in three of which Syndikat were totally wiped out, the flare was mysteriously launched (perhaps the flare came from Viper team? I doubt it, more on that in a minute...)
Phase 3: You are given your exfil order after "defending yourself" from Viper and scripted patrols start moving through all wooded areas in the vicinity of the village and the truck you have to reach. On my first attempt I moved west hopping from one forest to the next, carefully crawling past the patrols. When passing over a a forest road northwest of Namukava village a red flare was fired, shortly after I was opened fire on. On my second attempt I moved back to the insertion point and continued directly south to the shoreline, moving through the shallows and bypassing the village Namuvaka, I continued due west until I was roughly 250m south of the truck. From here it was a straight line to the exfil. During this entire trek I categorically encountered no enemy presence whatsoever. Despite this I still got a message that Raider 2 had just encountered the enemy (which is impossible)
So that's what I'm thinking atm, I think the scripted red flare during phase 2 is somehow related to this not unlocking. As I've described, the only other occurrence of a red flare in the mission is during phase 3 which denotes the enemy has detected you. I hope I'm wrong and that some people from BI can chip in. But I've completed the mission in almost every way I can think of, from what I've done I think this may be bugged.