From your 1st comment on this thread, the truck is stock except the extra tank, correct ?

With or without the Cat filter, since all the stock filters are in place, I don't see how they can deny the warrantee ?
Have you called another dealer, explained all this and see what they say ?

It's like you can be sold a vehicle with a warrantee and denied using the warrantee due to normal use.
Something here stinks to high heaven.