I know what you're getting at. But I don't think you will get a knowledgeable answer because no one has been through specifically what happens when visiting a dealer with A vs B tuner. Sure, people have been to the dealer and had their tune detected. But how an entire network of Ford dealers can recognize your tune as A vs B, installed by C dealer on D date, who knows. It's not like they plug in their scanner and it says WARNING COBB TUNE DETECTED.
I'm sure that if you have an engine failure in NY and you had a mp215 kit installed in PA then that NY dealer will try to contact the dealer you say it was installed at to confirm. Likewise, if engine failure and you lie and say it's mountune they'll figure it out before your ride is fixed.
Ultimately it's just humans working at the dealerships so there won't always be a black and white answer to every question. Bottom line is that the handling of mods is discretionary on a dealer by dealer basis. And no warranty is ever voided, you only run the risk of your warranty claim being denied for whatever repair you need. GTX1,000,000 turbo won't void my warranty claim for sync not working but when i throw a rod through the pan and want coverage they'll be like