How do we know if these will be warranty approved?
Read up on warranty law, unless it causes a failure, changing parts does not void a warranty (Magnuson Moss?).
You can also put back your stock equipment before you take it in to the dealership for a warranty claim.
To get the most out of an intake like this, a tune would be required and that might leave some fingerprints on the ECU but if Ford starts using that as a basis to deny claims, they will get a lot of bad PR.
I expect the STs will be handled a lot like Mustangs which get modified very very often. They also wouldn't put a failure prone engine in a sporty car, that's just begging for claims.