Ford can do all this stuff, but they won't. It's all a numbers game. They won't consume engineering resources over trying to stiff a customer a couple thousand dollar repair. It ends up being a net loss for them.
I have another example, my wife's old 2014 SRT Grand Cherokee. At 30k miles, its *third* transmission had failed. Intake, tune, exhaust. On trans 3, Chryslers FINALLY flew out someone to investigate the car. They pulled the ECU cal, saw it was tuned and... covered the replacement of the transmission entirely. There was a failed heater that caused the problem and was never replaced. It's all about cause.
Fords not gonna void your entire warranty over an engine calibration, but everyone knows that. Do you jeopardize you odds of repair when the block is windowed? Sure, but I've not heard of that happening stock or tuned. You do have loads of tuned guys having axles, diffs, and transmissions replaced under warranty here though.
I get what you're trying to say but it's not doom and gloom for a 3rd party calibration. Use discretion.