You are correct, it doesn't. However it does do it and when it does, well, have fun with that.
You say that you RARELY see a T1 Zekrom, and that pretty much makes it not BDIF. Then, turn around and say that you rarely see a T2 Magneboar set up, but all but justify that and say that, "When it does..."
So, I'm missing your logic in how "rarely" seeing a T1 Zekrom pretty much kills the viability, but rarely hitting a T2 Magneboar doesn't only NOT kill the viability, but some how makes it more legit by pulling of the almost impossible feat.
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Change gears
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I think as it stands RIGHT NOW, it is the clear front runner. But, as mentioned in so many other threads with this EXACT topic, that puts a big target on its back. That being the case, Samurott/Donphan seems like a very good deck for Nats. If I were going, that is probably what I would play....not saying it's BDIF, but I think it is pretty darn good and counters the obvious meta pretty well.