Since i could not find anything that goes in this direction and i got asked this a bunch of times by Duel Commander Players and i have nothing more than a guess i need an official answer.

If my Commander is one of the new Gods from WAR and dies and i decide to put it third into my Library and my opponent then casts Gonti and targets me with his enter-the-battlefield-trigger and takes my commander, can i choose to apply the Replacement effect from Rule 903.9
“If a commander would be exiled from anywhere or put into its owner’s hand, graveyard, or library from anywhere, its owner may put it into the command zone instead. This replacement effect may apply more than once to the same event. This is an exception to rule 614.5.”
instead, since the game always knows which card is my commander?

(This could also happen in Brawl with Thief of Sanity, but it would be easier to find out whether or not my commander was the choice)

Hi,

Thanks for your question. No, that is not an option. Since it's being exiled face down, the game doesn't know if it's your commander or not (since it has no characteristics), so you do not get the option of moving it to the command zone instead of exile. You don't know for sure that the exiled card is your commander, and being exiled face down means that the game doesn't know if it's your commander or not, so you can't try to apply the replacement effect to the card being exiled face down.

There used to be a rule that said if an opponent exiled a command face down and they could look at it, they must, and if it was a player's commander, they had to move it to the command zone, but that rule went away a few years ago. Now, if you let your commander go to your library and your opponent Gontis you, you risk losing your commander to being exiled face down for the rest of the game.

Thanks,
Nathan Long
Magic Rules NetRep