I started another playthrough yesterday and after doing the "do not open the chest, impaled heads part" I took the north route to get to Amadia's Sanctuary but to my astonishment the voidwoken encounter ("voidwoken: We meet again") wasn't there.
The waves of tiny voidwoken? That only appears in an ambush site -> e.g. it has to trigger. Run around the ruin full of oil-kegs and sooner or later they spawn.
Indeed. It must have been some sort of glitch. I returned later and they were there. I don't know why they didn't trigger the first time. I took the usual path.