Not to get too far off topic, but it sounds like your tune was just too aggressive / was a canned tune with flash revisions. This will almost always be the case with these types of tunes. Most tuners are trying to squeeze every last HP possible out of these engines at the risk of something bad happening or otherwise.
What exactly is "knocking" in your case? Were you monitoring ignition corrections? Anything less than a -3 is perfectly acceptable. Obviously you want to be as close to 0 as possible, but there are lots of things that will make an Accessport show negative corrections, including the vibration issues you are referring to. EQT is known to have pretty good tunes, so I'm surprised that your experience was this poor, but like you said, there are always quirks.
If you were experiencing excessive engine vibration, that was likely contributing to your engine knock that the AP was detecting. Putting 2-3 gallons of E was allowing timing to advance far enough that even the vibration wasn't causing the AP to detect it as a knock event, meaning that the AP was showing less overall timing being pulled. Also, be aware that the overall min / max figures on the AP shouldn't be a reference point. You should be looking at a complete data log to understand if your car is having a significant knock event. I've chased many vibrations showing false knock. It's a a PITA to chase down, and almost always causes more issues than it's worth. The stock tune is VERY reactive. It's perfectly normal for the car to pull 6 degrees of timing on the factory map, but these thresholds are much smaller when tuned. Think of it as simply narrowing the margin for error. The stock tune can make this kind of power at its peak if conditions are perfect, and if you have the fuel to withstand the conditions.
Even extended warranties can become void for tuning. I've seen these companies call the manufacturers to check on the case if they suspect that aftermarket mods contributed to the failure. Also, if you want a real tune, go get a legit dyno tune. You would be amazed how much of a difference it makes. UM does dyno tunes at select locations. Remote tunes with street pulls for data logging on Cobb APs just aren't that great. There is so much margin for error (bumpy roads, grade, fuel, etc.) that the tuner just can't see. If you want something reliable, go get a dyno tune from a reputable shop.