I can't stress how important after sales support is to apples success. Doesn't matter where you bought it from, either Apple directly or carriers, their direct service trumps others.
The Samsung issue could be a big deal. All the note 7s bought from various carriers, through carrier stores, retail stores like target, warehouse clubs etc it logistically could be a nightmare. What if you bought it secondhand through eBay, Craigslist, swappa? Sounds like a potential headache.
The carriers will still take care of it, even if you got it through 2nd hand like swappa or CL. I've had plenty of phones looked at and even replaced which I bought 2nd hand and no one even asked me where I purchased it. Heck I've even had them cross replace, I brought in a broken Tmobile Note 5 to AT&T and they replaced it with no questions asked. I think all they really care about is that you are a paying customer. I doubt the carrier pays anything at all for the warranty exchange, it just goes back to Samsung.
I still don't see what the advantage to Apple's customer support is. With one exception though, Apple's screen replacement cost is a lot less than Samsungs so I could conceivably forego Apple care on the risk that I may break my screen once during ownership. But besides that there really is no difference while you are under warranty.