Well it seems like you guys nailed it with whirlpool adding more IBUs. I received a reply from Matt at Avery:
"You raise a very valid point with our clone recipes. The fact of the matter is alpha acid utilization doesn't scale down very well (or well at all), nor do the processes involved. The recipes on the website are solely a guide and knowing all of the different ways of doing things out there, it would be impossible to come up with an exact clone recipe for everyone.
Also, concerning processes, I would like to add we are brewing on a two vessel system and our kettle doubles as our whirlpool. This means we have a residency of over 1.5 hours of hops sitting in near boiling wort after we kill the boil and add our aroma addition; therefore, we get a ton of IBUs from our aroma addition. We have done extensive testing with our IPA on the lab's spectrophotometer and actually exit the kettle at ~130 IBUs but the yeast does a great job of bringing them down to ~70...but that's another story. In fact, due to the amount of time in the kettle/whirlpool we get over 75% of our IBUs from the aroma addition.
Thanks for the inquiry and if you have any other questions please don't hesitate to ask.
PS: You may or may not know this, but we actually list clones for almost all of our beers on our website (same IBU discrepancy rules apply): http://averybrewing.com/brewery/recipes-for-homebrewers/
With this information I messaged Tasty McDole and told me when he was doing the CYBI show they would would add flame out hops at 20 mins to go to compensate for 30 mins of whirlpool.