If she is making you feel uncomfortable and she is not explaining everything to you so that you feel comfortable in EXACTLY what they are doing walk away. Use their quote on the car, call another Toyota dealer and tell them to beat the price. Tell them you have the financing ready and you are willing to pull the trigger as soon as they beat that price.
In today's times, they should be begging you for their business and should make you feel comfortable. Don't let them blanket over everything with "oh, this is just standard procedure." B.S. If it doesn't make sense to you its not the deal for you.
And having said that, yes, you might later on learn that what they were telling you was true, but if they can't explain it so it makes sense to you at the time, its not worth the risk.