Yes it would, in short.
Basically the Gear 1 was nice because you could root your device, then root the Gear 1 because it ran on Android.
However, the Gear 2 runs on Tizen, Samsung's OS, which at this moment as far as I know, doesn't have a root method.
Rooting your Android device then leaving the Gear 2 on Tizen will make the Gear 2 unusable.
However, I know some ROMs that support Gear Manager, it's just random on whether the device will be able to pair up with it or not.