(TADC spoilers avoidance text)

For me, the ending worked because it's something they must've suspected as far back as "Beach Episode." After Abel spun them that whole scenario with the VR pods, somehow it felt a lot LESS likely that the crew were really experiencing this as VR. Plus, all the little hints over the series that their minds can be edited like software. Then, in the next episode, Kinger talks about Scratch's brain-scan project. I think at that point everyone realised what they were, but nobody could face saying it aloud.