Hi Simon, I'm not an expert, but our experience was similar. a couple of weeks ago. We hadn't uploaded the documents, we paid for them to scan. They just took all the originals at the biometrics appointment, scanned them all and handed the originals back, and the visa's subsequently been approved.
If one of the more experienced contributors on here haven't said otherwise I'd assume it's all ok.
(my wife didn't get told not to leave the country either, though she was quizzed quite intensely on her opinion of the NBA's MVP!)