I dunno man I think when push comes to shove its really all dependent on how the dealer treats a warranty issue - I wouldn't put THAT much merit on 3rd party warranty claims. That being said, while I've heard of people getting pushback for warranty work due to TQ arms in the rear end, taller/stiffer front springs, larger FMIC, for all the concern & questions honestly I personally have yet to hear from ANYONE having an issue w/ warrantied drivetrain work due to a tune. That's not to say it can't/couldn't happen - I just haven't heard it. I had warranty work performed on my previous tuned 2018 Raptor - I tuned back to stock when I had it done - but didn't dealer wasn't going to dig into it one way or the other, they just ID the issue & (esp if there's a known TSB or its a common quirk) they just move forward w/ the repair & call it a day. The 3.5 ** has a forged crank, it has PLENTY of fueling capability in stock form for a tune-only setup, & w/ a tune from someplace like gearhead or goose or livernois, in many ways I think they help PRESERVE the tranny/transfer case vs. the stock programming IMHO.
My 2018 had the Gearhead tune for 28k miles w/ 0 issues (other than a chick broadsiding me @ 40 mph totaling it....which wasn't tune related lol!)
Either way - I think your mindset of driving it around stock getting used to the new truck for a few thousand miles before doing any mods is a good one. Enjoy the truck!