I don't think the warranty will be voided. Especially if one has nothing to do with the other. For example. if you get an intake, they can't void your warranty for the engine, or suspension or something.
But, just to be safe, keep the stock system. You'll never know. Someone might need to purchase it on another board.

As far as that other intake system you've seen...with two filters. I've never...never seen a set up like that.
Are you talking about a intake system on a turboed car?
They would have a filter a the end (Normally the turbo is right before the filter) and you may mistaken the 2nd intake (on the long pipe from the throttle body) for the B.O.V.

Something like this setup