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"They will only appear in the second location after you complete the quest: The Forest Kingdom (I don't think this is true, I haven't done the quest and I found them.)"
There are three spots marked on the map. After beating them at the first one (atop the Goliath) they escaped and then I couldn't find them at the supposed second spot (near where the flight units were) but I did find them at the third one (below the bridge) and I have not done The Forest Kingdom.
Same here.
I found them first on the building you dropped in at the start then I finished them off at the entrance of the factory. Also I have not even reached the quest The Forest Kingdom.
it seems they only occasionally show up? i haven't even inspected the flooded ruins yet (i've been working on some sidequests to declutter my map), but here's my info, however helpful it may be-

i get the quest, i try to clear some sidequests. head for the closest one, up the goliath. very first spot i check and they pop up, then flee, per the norm. i do some other sidequests, check the starting area, comb through the entire building and check out the starting area. nothing. go to finally reclaim my body from the factory, they don't pop up when i go into the designated area either. nor do they pop back up on the return. do some more sidequests. finally, they show up at the starting area on the second run-through. as a note, they only spawned when i went to the right corner of the roof, the one on the building right in front of the ramp there.

hopefully this helps? i've only done this once so i realize things could use some verification, but it's something.
You have to finish the machine quest with the big dude