Doorsill:
Pictures don't provide a sense of the penetration of the rust, which fortunately was shallow on a 3-month old car. I was able to easily sand the projection (where the clips mount) to bare, corrosion-free metal, then mask, prime, and paint it with spray cans. For the top 3 coats, I used some red paint purchased from "Benny's" for $1.00 per can. It matches amazingly well, and is hidden by the trim anyway. I spread the clips slightly with pliers, then epoxied them in place. I don't expect rust to return in those particular spots. By the way, this issue of trim-mount clips compromising the paint protection is not new or unique to Ford. In the 50's and 60's, it was not uncommon for windshields to become loose (and/or leak) as the clips used to secure the decorative chrome surround caused the metal around the windshield to rust away under the molding. Since manufacturers have eliminated those moldings, this is no longer a problem.
Instrument panel supports and braces:
The rust is also shallow, but not easy to access and sand without disassembly. While at a wrecking yard removing some parts from a '98 GT convertible, to use for customization projects, I had the opportunity to check out the condition of the same under-dash metal on a 5 year-old vehicle. The rust was pretty bad, but in no danger of immediate disintegration.
The "A" pillars use a metal clip affixed to the garnish molding that fits into a slot cut in the underlying metal. Same problem as the door sill, but not as bad, as the scratched area is confined to the inner edge of the slot.
Forget the notion that Ford would have any motivation whatsoever to change manufacturing practices. From their viewpoint, the ideal car is one that begins to fall apart the day after the warranty expires. There is a lot more profit in the sale of replacement parts than new vechicle.
Where have I found rust so far?
Wherever metal trim clips are used.
Suspension components. Fuel and brake tubing. Brake calipers. Parking brake cable. Brake and accelerator pedal assemblies. All under-dash structural metal. Steel sheet metal used to reinforce the door trim panels. Steering shaft and joints (under the dash). Console mounting brackets. Seat frames.