I believe to do this justice, I won't answer for a a lot of things you addressed. I should note that Colin apparently added the clause in the game, so there really shouldn't be any complaint anyway. This makes both your post and my post moot, but I'm willing to go forward anyway.
However, I need to address one particular point because it applies directly to my argument if you don't mind. >_> This is simply a rehash of earlier arguments just in case you didn't read every post in this thread.
If it's proven to be sitting there, waiting for us to use an item to battle it, why should we wait and twiddle our thumbs and wait for Nintendo to give us the thumbs up? If its stats, moveset, sprite, etc. are all programmed into the game, it should be acceptable. The 'Hypnosis + Brave Bird Crobat' argument doesn't fully apply here, as we have ABSOLUTELY no evidence that Nintendo will plan to give us this option, while there is certainly evidence (though no proof) that Nintendo will continue to milk the cash cow and give us an Azure Flute giveaway.
There is no proof, and at the same time I hope I have laid down an argument that shows that Nintendo might not even release Arceus. If it is a debug pokemon they have no reason to release it in the first place and the flute would serve as a mechanism to prevent the typical person from using it.
There was also another point a few pages back that even if Nintendo planned to release Arceus, they have reason not to do so. Religious tension is very high worldwide and to quote the absurd example again,
a woman was jailed for naming a Teddy Bear Mohammad. (with a link this time, so no one is insulted) Considering that Arceus is a god in Pokemon world, it would do them some PR to simply never release anything associated with Arceus. I mean hell, does Nintendo want to send the message that humans can not only capture a god, but bend his will to your will?
Both of these viewpoints are compadible with "milking the cash cow" conjecture you laid out. In the debug theory, Arceus already saved Nintendo tons of cash by lowering the amount of development time, and in the PR theory, not releasing Arceus will allow Pokemon to last perhaps another generation or so without people complaining about Religious connotations trapped in the series.
Either way, we won't know until Nintendo releases Arceus. Only then will we know that Arceus is
canon like Manaphy, XD moves, and NYPC giveaways.