OP, you keep mentioning "comprehensive" warranty. That is a smokescreen word that means nothing outside of what is actually in the fine print. Best to get that notion out of your mind if you don't want to be unduly influenced.
Personally, I don't think that the fact that the dealer issued it makes much difference. Lots of very shady dealers out there...
I would look at it as not being much relevant to your offer figure, basically. Just think of it only as a potential pleasant surprise backup plan. Would I pay the $50 transfer fee? Yea, maybe if the dealer looks OK. Cuz that's cheap. But basically I would go in not counting on it to cover me much at all.
However, it's worth remembering that many sellers are influenced by emotions. It is likely a bitter pill to swallow for the guy to have spent 4K a couple of years ago so that may indeed make him stand his ground, whether rational or not. You may want to think about how to handle that. Nothing wrong with ostensibly offering 2K for the warranty if you price the truck 2K below FMV... If that makes the guy happy and ready to deal. Kinda like what dealers do with trade-ins, in reverse.
Finally, you surely know this already but do keep in mind you are buying an inherently very expensive old vehicle that will likely take a ton of money or a lot of DIY to keep running. Very good, sure, but possibly very costly to run. (Which is of course the fear that those shady warranty companies count on...) You will be shocked by the bills if you have to rely on dealers to keep the beast on the road. Best to keep that in mind when deciding on your offer.
Good luck!