This is the reason that you'll never find an egineer in the sales or marketing department
Sometimes it is in the best interest of the company to absorb the cost of a repair like this even if it "probably" was the fault of the customer. Trust me, this guy does not have the final word in regards to when to cover something under warranty. The only reason he was involved at all is because it is a new engine and they are still working out some early production issues.
Really? I know plenty of engineers in Sales & Marketing in the auto industry.
I worked as an engineer at Chrysler for 12-1/2 years and believe me, if they want to do the right thing, they will. However, it sounds like you have a fight on your hands and you can thank your dealer for not going to bat for you in this case. It starts with them.
Depending on the situation, engineers of various levels are sent out to the field to evaluate failures. I've personally seen parts replaced that were out of warranty because it was a condition that was of no fault of the owner/consumer and it was the right thing to do.
Follow the advice above and chase it up the chain (and yes, you need to do it calmly or you will be dismissed very quickly). Get your story down on paper and contact anyone you can, and be extremely detailed and leave nothing out. You'd be surprised at what seems like a small, insignificant detail and how it can somehow be the saving grace. A word of caution - don't try to bull#### anyone, they've likely seen about every type of failure imaginable and if yours is as stock as you claim, it should be fairly easy to diagnose.
Try to find out if the engineer was a regional guy or someone directly from the V Engine group in Dearborn. Maybe I missed it, but have you tried to contact him directly? He may be able to shed some light on it for you if you can get ahold of his email and chat.
Bottom line - don't give up and leave no stone unturned.