Frankly, the Stage-1 download is a waste of money. The fuel is not greatly affected. The rev limit is raised, but I am dubious about the value in that, unless you will be racing. Adding fuel is best, notwithstanding a Stage-1 download.
As far as being told that a Dobeck tuner invalidates your warrantee, you have the Moss-Magnuson Act (available on the web to read, just Google it) to back you up. I would contact Dobeck, and tell them what you are being told and the name and phone number of the dealer is, in case they want to contact them to straighten them out.
Enjoy,
Rich P