Well, technically Canon could do an about face on policy tomorrow, stop honoring repairs on lenses not bought from authorized dealers (like Nikon), and you'd be screwed. Or, they could stop honoring warranties on items not purchased via authorized channels. That's unlikely, but, there is more than just ink that makes the difference. I wouldnt pay hundreds more for that difference. But, Amazon was just selling the authorized version for $699, so I'd go that route and pay the extra $60 no doubt. Especially for the risk you get a lens that is misaligned or has something DOA.
If something is misaligned or the lens is DOA, you should return it to the vendor. Warranties are not for initial product failures. They're to cover you after the store's return period.
You should never repair a brand new product. That's tantamount to paying new prices for a refurbished item. If you're going to get a refurbished item, you should pay refurbished prices. If you pay for a new item, you should get a new item in working condition.