At times like these, I think it might help you to look at your username.

Flash-froze*

That was the worst part of this premiere for me; any ridiculous hopes that the vortex would erase Arrow S3 were erased so abruptly.

True, unfortunately I missed the point I should have made: that even if this doesn't end up fitting logically in the universe such moves aren't very egregious if they add to the point of the episode, which I think this twist does. I mean, how much does this inconsistency matter when compared to what him being real…

1. He's probably an alien (as Beard said).
2. This show lives on the idea of multiple universes.