I suggest that if the savings would be a few thousand dollars that they are using a lower grade of shingle then you would get if done by the company its self.
Also the warranty is more than the shingle quality. It is also for the workmanship.
I had a leak in the valley of my house. Turned out to be caused by a clogged gutter but still the company came out to diagnose the problem and if it had been the valley they would have repaired it. Later when I had a new roof put on I learned that there is a better way to do the valley and if I'd had a problem unrelated to the gutter the company would've redone the valley.
I had a home warranty on our home in AZ. There was a problem with the roof and the home warranty covered it. The price for a home warranty was less than $500 and well worth it. You might be able to get a home warranty that would cover the roof. I think it was American Home Shield.
Bottom line if you decide to go without a warranty is to be sure that you're getting the same quality of shingle that you'd get with a warranty.
Personally, I'd go with the warranty.