Are you being scammed? No.
The reason your credit score is different, then the one the dealer pulls, is because the dealer will get a score that is auto specific. When you pull your credit, you get your overall credit score. When a dealer pulls your credit, they get your overall score and an automobile risk score, this risk score will usually be lower.
So no, you won't have the same score.
Why the warranty?
Because Toyota financial offers a 2.9% rate, on pre-owned, factory certified cars. There is a warranty inspection that needs to be done to qualify as Factory Certified Car. This is the warranty the dealer is telling you about.
It is all true, if you buy the warranty, the dealer will pay to have the car certified through Toyota and then Toyota will offer you 2.9% on the certified car. This is done everyday and it is not a scam.
The factory charges the dealer $750 to certify a car, so the dealer does not want to pay for that certification, if the customer is not going to take the 2.9%....Who wouldn't take the 2.9%? Cash buyers, bad credit, that can't qualify. The dealer doesn't want to pay the $750 fee for no reason, so they make the customer agree to the warranty first, It is all good and you are not getting ripped off. You just have a bad finance guy at the dealership that doesn't know how to explain things....
Source: I ran the biggest and most profitable finance department in the country. Also, I ran finance for Toyota.