Joseph Kriz - I think you've misunderstood how IR Remote pairing works. Unlike Bluetooth - which is a two-way communications standard, the IR remote is a send-only device. The way pairing an IR remote works is totally different to a Bluetooth product.
The Apple IR remote control has no what it is paired to (or if it is paired). The pairing works because every Apple IR remote has an 8 bit Device ID, so that every button press is sent with an ID for that remote. A different remote will send a different ID. (There are 255 different IDs. If you are unlucky enough to have two IR remotes with the same ID it is possible to change the ID of one of them by a button combo on the remote)
More details here : https://en.wikipedia.org/wiki/Apple_Remote#Technical_details
By default Apple receiving devices - Apple TV 1-3s, Mac Minis and other Apple IR devices - ignore the ID and accept input from any Apple Remote irrespective of its ID.
When you pair a remote to an Apple TV 1-3, Mac Mini, or other Apple product with an IR receiver, you are simply telling the receiving product to ignore codes received from any remote with an ID other than that you have paired it with. The remote will still work and control an unpaired device, so the rule is normally that you need to pair every receiving device with a different remote to ensure you avoid interference. (You can't assume that a paired remote will only work with a single device once paired - you have to pair all receivers too)
The issue with the Apple TV 4th generation is that it doesn't have the ability to pair to a specific IR remote BUT does have IR remote functionality built in. So if you have an existing Apple TV or Apple IR remote controlled product, even if you have paired the product to a specific IR remote, your Apple TV 4th gen will also respond to it.
This should be a straight forward thing to fix in a software update though. It's just surprising it wasn't spotted during testing.