That matches what I found too. I contact FP as Well as Fords ESP department. Ford ESP pretty much said the tune, although a Ford Performance Accessory, is considered "aftermarket" since it wasn't factory installed. If a failure was attributed to the tune, it would not be covered.
I think in practice though it would be much less likely an FP tune would drive a powertrain warranty void for a couple reasons. Not saying it wouldnt happen but when i look at the risk/reward of the tune this is how i plan to approach:
1) OEM source, if the FP tune started generating issues it would be publicly embarrassing to them, its not like a 3rd party source, customers will expect factory like quality. Nothing would drive attention to the FP tune causing problems more than denying powertrain warranty claims, Ford the brand would take the heat for their own product, not a good look. My bet is with a FP tune they will be DAMN sure the tune caused an issue. Contrast that to a 3rd party tune where the default will be the opposite, put ANY borderline issue onto the tune.
2) FP engineers are going to be more conservative, for both the above and because this is effective R+D for future calibrations. They aren't going to be targeting more power at any cost.
3) they are warrantying the tune to some extent, so it has been design to protect the powertrain components for a period of time without failure (read within ford acceptable failure tolerances). which goes back to #2
