The scene has 3 trigger locations;
- The bridge to the Goblin Camp
- The dirt path to the Mountain Pass left of the Goblin Camp
- The bridge guarded by the Githyanki patrol
Once the party experiences the Absolute's voice for the first time, the next long rest will be the stage 1 ceremorphosis scene + the Guardian swooping in. If one doesn't take a long rest though and tries leaving the act, it will trigger immediately too.
As for my head canon, personally if I don't munch any tadpoles then I like to think I'm fully pure afterwards. And if I do munch them, then I'm just better and slightly evolved.