It's a good rule of thumb to only have warranty work performed by the dealership. Dealerships require each department to be it's own profit center, which drives up costs.
It's a good idea to find a reliable mechanic shop (one with a specialty in Toyota, if possible) and use it for all non-warranty work. You'll find your bills reduced significantly.
A good example of what you've experienced is that I once had a Cadillac's battery go out while the car was under warranty. I took it to the dealer and, although I wasn't charged, the dealership noted that the cost of replacing the battery was $354.00.
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