I do think it is conceivable that Apple could reject apps for this.
Maybe they will decide that apps have to provide their functionality with just the stock Apple TV, without requiring any external devices.
The fact that they decided to prohibit games that require a game controller hints at this.
I am not saying I think that this is what will likely happen. But I think it is possible and at this point I would not want to invest significant time and/or money into an app that relies on auth via external devices.
Unfortunately the fact that some app (especially a pre-tvOS app) does something is no guarantee that reviewers will allow you to do the same.