First I think a lot of this depends on the people you interface with at the dealer.
2nd, Stage kits are not sold by Mopar, they are Mopar Performance, 2 different entities. I doubt they will have an issue with a stg 1. Before I bought my PT, I talked to the service manager and asked him and he did not have a problem with it. He did say the new PCM and injectors with the stg 1 kit(03) would not be warrantied but the rest of the engine and drivetrain would be . He likend it to a plow set up they install on trucks, the plow wont be warrantied(by Mopar) but the truck will be.
Since PT's are limited to Stg1 , I dont think you will have many problems.
THey must be getting a lot of warranty issues on SRT4's because of poeple modding their cars with all these tricks.
Also think of the poor techs who have to troubleshoot problems and dont get compensated for the time they spend diagnosing something after jr removes his MBC which he didnt set up right and overboosted his engine and roasted a piston.
Of course the document looks like a how to
Mike