Well, it appears there is no clear answer to this question.
Seems best to look at it not as black and white, but in terms of probability. If you do several mods to your warranty
stang, then you will likely not expect your warranty to cover everything anyway. For example, add lowering springs and it would be difficult to argue your struts, mounts, panhard, etc. should be covered under warranty, right? Those parts, likely (say 75% chance), become your responsibility. On the other hand, to say your Eibach springs caused your transmission to fail, would be less likely, although feasible (say a 25% chance of not being covered).
You could likely stretch these odds in your favor a little by either finding a Ford service that was friendly to mods or, as some have suggested, only take your car to Ford service when you need warranty work or a recall (then be sure to reverse what you can, before hand).
So, yes, it is a crap shoot in a way, but there are things you can do to move the odds in your favor, BUT NEVER to a 100% level of certainty. If you need that, I'd say stay away from all performance mods.
Note: By "friendly Ford service" I mean some places do a lot of mods, others do none. Definitely worth checking before you bring you car in. Of course, I live in the LA area and there is a Ford dealer every couple blocks it seems (really, about 15 within driving distance). You may not have as many options.