OK, I've finally got it.
Have read multiple posts on this topic (tune & warranty) and the more I read, the confuseder I became.
So,,,,,,,,,,,for anyone else a little befuddled about this, here's the skinny:
1) Mountune sells the Ford approved tuned AP for $999, which INCLUDES an airbox which MUST be installed as part of the process by a Dealer or ASE mechanic
2) Mountune also sells a Cobb tuned AP for $499, which comes with their drop-in filter and you can install at home by just plugging it into the OBD port. However, this isn't approved by Ford.
So bottom line, you pay $500 (plus installation) more to keep your warranty. And they throw in an airbox.
If I go this route (tuning), I'll probably just go with the Cobb and take my warranty chances.