I believe if you look closely, your manual says that you can use a synthetic oil but that you must stay with the 5,000 mile maintenance schedule.
As far as changing the oil too soon, Toyota does not use a "break in oil". You can change it anytime before the scheduled change that you wish. I normally change my cars every 5,000 miles anyway with a new engine being changed at the 2,500 and 5,000 mile mark for the first two.
To be honest about it, using that schedule for changes, it will not make much if any difference what oil you use. Dino, Synthetic, blend, Amsoil, Mobil 1, Rotella, whatever you use should make the engine last the life of the car.
Once your warranty period has expired, feel free to increase the mileage to what you like. Some of the guys I know go to 12,000 or 15,000 miles between changes using a premium synthetic. As long as you use a good filter (Puralator Pure 1, Mobil 1, Amsoil, Wix, etc.) and check the oil level often, these motors will last a long time.
This topic is one that will never be resolved and each person needs to do what they are comfortable with. I am known to be anal about car maintenance thus my 5,000 mile changes. I like doing them and that is fine. Others like going longer, some change every 3,000.