my understanding is that if nothing looks strange, the robot send the pass. If the robot is not sure, it will pass the file to a human for further check.
Stuart is right, this part is for foreigners living in another country, but the web developers missed the point and made the field mandatory. So upload your passport and you'll be fine. Many did it before you.
It's not like the US visa, you can't enter Thailand with the visa on a different passport. You'll need to ask the embassy to transfer your existing visa to the new passport.