You need to understand Toyota manufacturing process.
When they build new cars, they do NOT perform or check alignment on every new vehicle. They just assemble them under the assumption that if parts (suspension, frame) are within specs and the adjustment cams are installed in the "dead center" position, the alignment should be OK. In case of some production lines a check is performed automatically using non-contact metrology equipment, but this is usually reserved for high performance or luxury vehicles (think Lexus LC500 and such). For most mainstream Toyota vehicles, they only spot check a few vehicles from a production run to look for systemic errors.
So it's quite normal that a most new Toyotas come out with alignment that is far from perfect and barely within or slightly out of tolerance. Because the misalignment is small, this may not show as uneven tire wear until you have accumulated a significant number of miles.
Alignment is covered under new vehicle warranty for 1 year / 12k miles.