Sounds like they'll spec how the bus however you want it. I like the look of the plain white. And having no interior would be a great blank canvas to start with.
You might as well order what you want since I bet finding one used would be next to impossible. Thomas probably sells 100 or more yellow school busses for every one of these.
If you are going to have them "custom build you a blank school bus". Make sure it is a 4x4. What is an extra $10k+ also if a got a little more extra $$$ go for a steering set up like this: