Some really don't care. I've personally seen trucks wrote up for bad headgaskets/egr cooler/oil cooler the whole 9, on a perfectly good working truck. They roll back out of the shop with ARP's, EGR delete setups and what not. Said dealer, stocks ARP studs, and liberator EGR deletes. You buy those parts from them, you get them put in on Ford's dime... a little dirty if you ask me, but I know a few happy guys driving 6.0's because of it. The trucks don't go back in over and over and over for the same repairs either, because the shop did it right the first time. So while they might be putting the blinders on to Ford, I bet in the long run it saves them some coin.
I also know dealers that will do it legitimately, unlike the other "said dealership". I've had studs put in under warranty, after my gaskets blew initially. I've also had them taken out under warranty after those blew...
Some dealers wouldn't look at my truck cause I had gauges, and stacks. I've also had some try to blame issues on my vegistroke (which I did not hide in any way), then when I show up, they covered it under warranty!?
It's a crap shoot. Try and find a tech in your area and become GOOD friends with him. A tech buddy of mine gave me some good advice before: "Tell the service manager as little as possible, and the technician as much as possible". I give this tech a printed list of every mod on my truck, he wants to know so when he has to pull the cab he doesn't damage things like trans temp cable, or EGT probe, or anything of that sort. The tech is the guy out there turning the wrenches, not the service manager!