I am well aware of the wording of Ford's warranty since from 1990 to 2001 I was a employed as Ford and Lincoln Merc service adviser . As Ford's warranty is worded any aftermarket component whatsoever voids the warranty, so technically the hundreds of aftermarket remote start systems that Ford dealerships install on new cars everyday voids the warranty.
....... why is the damage always limited to the the #8cyl ? If it was a bad tune, say for example it caused a lean condition shouldn't there be damage to the other pistons ? Could there be an inherent weakness in the engine? The 5.0 should be a more robust engine then the 4.6 yet there are thousands of 05-10 4.6s running around more heavily modded the the OPs car without issues.
What a coincidence, I started working for Ford in 1990 also. The big difference is that I still work for them (dealer, not FoMoCo). Ford's basic warranty policy of only covering manufacturing defects has not changed since 1990, is much older than that, and will always be the same. However since you have stopped working for them, there have been a ton of of changes to the details that go beyond that of the basic policy.
When someone modifies their vehicle, which could be by installing a supercharger for example, the warranty is not automatically voided as you have implied. If this supercharged vehicle goes to a dealership with some form of powertrain related failure or other concern which could be considered unusual and directly attributed to abuse and/or the modifications present as determined by the dealership service personnel and/or Ford factory representatives in some cases, then, and only then will voiding the powertrain warranty be considered. Even if this does occur, the remaining components on the vehicle are still covered under the same terms as they always were for whatever time or mileage that remains. The mere act of bringing a modified vehicle into a dealership service department is not going to end with someone having their warranty voided.
As for dealerships selling vehicles in which the modifications are performed by the dealerships themselves, if the component installed was made by Ford and/or sold by Ford then Ford will warranty the part from defects related to manufacturing, not installation, and they don't warranty the installation alone in any circumstance. It is up to the dealership themselves to warranty the actual installation. If a dealership has installed a part that was not sold by Ford, then Ford won't warranty that part (this should be obvious). If something fails on a car in which the failure can be directly attributed to modifications that were performed by the dealership, then the dealership is responsible for repairing this failure at no cost to the customer. Any dealer that attempts to submit a warranty claim such as this last example to Ford and cover up the fact that the failure was a result of modifications done by that dealership, would be committing warranty fraud is and subject to very serious consequences.
Seeing as how you worked for Ford over a decade, you should already be aware of everything I have stated and none of it should come as a big surprise.
On your question in regards to the #8 failures on 5.0's, I will explain:
From their inception with very, very few exceptions, Ford does not now, nor have they ever designed vehicles with any consideration of any kind as to whether consumers wish to modify their vehicles after purchase or race them in any way. The very few exceptions to this rule, did not carry any warranty at all, or had a very limited warranty.
With that said, no engine ever made is perfect. That needs to be stated again - no engine ever made is perfect. Every engine ever made has minute differences from cylinder to cylinder as far as compression, air-fuel ratio, combustion temperature, and differences in structural integrity in the block & cylinder heads all on even the best engine designs ever conceived. This is a fact. The 5.0 as sold by Ford in stock form is a damn good engine, and being it was derived from the 4.6 (which was one of Ford's most reliable engines), it will also stand the test of time. The 4.6 3-valve engine had 9.8:1 compression. The 5.0 coyote has 11.0:1 compression. This increase in compression combined with the addition of TiVCT (twin independent variable camshaft timing) on the new 5.0 has resulted in an engine which is closer to running on the ragged edge then the 4.6 ever was. This is evident because the 5.0 in naturally aspirated form does not pick up much horsepower when modified in comparison to older Ford engines that pick up pretty good HP gains while still remaining naturally aspirated. Taking all this into consideration, there is very little margin for error when modifying the 5.0 in comparison to to previous engines. #8 cylinder on the 5.0 runs slightly hotter than the other cylinders which is a completely normal variance (as I explained earlier), and is of absolute no concern on any completely stock engine. Taking this normal characteristic of the 5.0 in combination with people trying to get much higher horsepower output into consideration, and an all new design valvetrain that is exponentially more complex, quite a bit higher compression, and you have a recipe for disaster when dealing with less knowledgeable / less experienced tuners, aftermarket suppliers, engine builders, and so on. Detonation is the specific problem, #8 cylinder being the most susceptible due to the reasons I posted. In some instances, other cylinders do in fact show damage, not just #8 cylinder. The FRPP tune for 2011 & newer Mustang Gt's only gives you about a 16HP gain because that is all the FRPP engineers are comfortable in giving you. Whereas a lot of companies in the past got by with moderate success on other Ford engines such as the 4.6, this isn't the case with the 5.0. You really have to know your stuff when modifying these engines. It's as simple as that.
I am not Mr. goody two shoes over here and telling people not to mod. their cars. My only intention is to let them know the truth, and to let them know it's not a good idea to modify your car if you really care about your warranty.
Just because a company sells a tune, sells a part, and makes all kinds of claims about how great they are through big impressive advertisements or has thousands of posts on some online forum, and what huge horsepower gains you will get on your 5.0 if you spend your money with them does not make them an expert, or qualified to do so in any such manner. Anyone can make such a claim, and any past success and/or reputation they might have with other engines is pretty much irrelevant when it comes to the 5.0. If it were me and I didn't care about my warranty, I would stick with FRPP, Shelby, Saleen, Steeda, Roush, and as I have come to learn, MMR really knows their stuff on these engines also. MMR in fact, as has been stated, does have a kit to modify the 5.0 cooling system so that the #8 cylinder detonation concern doesn't reveal it's ugly head on all your 1000HP+ quarter mile killer monsters out there.