If the warranty you're talking about is the
RV Warranty Forever, I'm guessing the annual inspection of bearings and roof, etc. probably will cost you over $500 and possibly a lot more. Interestingly, their list of what's covered doesn't help you with bearing or axle problems, or roof/structural problems, even though they require an annual inspection on those areas.
It might be good to have those inspections done, but I'd guess they count on most owners balking at a big annual expense and abandoning the program before they have to pay a 2nd inspection bill.
If this is the warranty you're talking about, do you know the price of your first inspection? Are you prepared to spend that much every year?
Another consideration about the roof replacement is that it's very invasive. The A/C units, vents, fans, ladder (if you have one) have to be removed. The rubber roof is pulled off, damaging the luan under it. They'll sand and patch, and maybe put in a new luan layer, followed by a new rubber roof. At the factory, the Dicor roof is extended several feet front and rear and then covered by the caps. For the repair, they will cut the roof at the cap line and create a new seam there. That'll leave you with a much greater possibility of leaks as the caulking wears. There's a lot of opportunity for error in this process.
With respect to resale value, the question is what's worse to a potential buyer? A piece of tape, or knowledge that the entire roof was replaced. Hard to say. But I'll bet if you apply Eternabond and later trade the rig, the dealer will no doubt explain to potential buyers that Eternabond is the greatest product ever invented.