That is what SCT and DiabloSport hopes you believe, but unfortunately, it isn't true.
All Ford needs to do, it so prove the parts are performance oriented, and that is pretty easy for these types of items.
The Magnuson-Moss Warranty Act has multiple sections, and it is one of the other sections which aftermarket companies like to pretend doesn't exist. That section allows manufacturers to fully void a warranty if there is any evidence of abuse. Unfortunately, performance parts are considered such evidence; if you have them you must be making use of them.
Now, if you have a good relationship with a particular dealership, they might just look the other way. However, if they don't, you can't force them to.
As to parts Ford itself sells, well, they are a special case. Ford does allow those to be installed, and not affect Ford's warranty. Yea, they can be the exact same part you can buy elsewhere, but Ford adds to the price when they sell it, the cost of the extra risk.
Pick up the latest Muscle Mustangs & Fast Fords. There is a good article (written by a lawyer, but not intended to be legal advice) describing how dealers can/will screw you. It also describes your options in resolving the problem.
If you look next to the part number there is an "*" and upon looking at the bottom of the page, it states "* Not legal for sale or use on pollution-controlled motor vehicles." Sounds to me like this would void the warranty if you had a part failure related to the the newly installed parts. You might also want to read the "Warranty and Use Information" link on the bottom of the page. The Magnuson-Moss Warranty Act is pretty clear on that a parts failure must be the cause of the other part failure to void the warranty. Of course, everyone will have a different opinion on what caused the part failure and you will probably spend more money figuring that out than replacing the failed part. Just my two cents.
It'd be very hard to void an entire warranty. These mods affect parts that are under warranty and do necessarily say VOID on the whole thing. If you have a CAI for example and your radio stops working, Warranty. If you have that same CAI and your car starts running poorly because of it, THATS not warranty. The warranty doesn't cover if your car breaks just because. The warranty covers your car if it breaks because of a factory defect and because of Ford.
Now, if you have a CAI and tune and wanna be sneaky sneaky just put the stock tune back in and unplug the battery. Some times you might need to go througha drive cycle which some times includes cooky things like rolling to a stop without hitting the brakes from 30mph or some BS like that. It will give a code saying your battery was unplugged but all you need to say is that you left your lights on or something; Ford can't prove anything after that. But yes if you have a tune it does do bad for your warranty. If that tune is found to have caused the problem, oops you gotta pay the Diag. fee, the cost to repair it, and whatever else the dealer throws at you. Its not Ford fault why should they pay for it? So in the end just think about it. Yeah they can screw you over, yeah it may be your fault, or yeah they may help you out.