So if it is legal in my state or the state the bus is registered in to keep it school bus yellow, can another state bust your balls about it if you are traveling through?
NO!
You are governed by the registration laws and laws regulating school buses in your state of registration/residence.
It is a good idea just in case you have some "Splaining" to do to nice officer especially when traveling out of state in your bus with the original paint/livery/markings to carry a copy of any laws/regulations concerning school buses and their operation in none-school use situations in your state of registration/residence
The ONE exception to my NO answer I can think of could possibly be that you lived in a state with NO school bus paint/marking restrictions or regulations for none in-service school buses. The bus you purchased was from a state WITH paint/marking restrictions and that bus was still in the original paint/markings from that state with paint restrictions and you were traveling through that same state with your out of state registered bus which was in originally in service in that state with paint/marking restrictions with your bus still having the restricted states in-service bus paint/markings.
It would be possible/probably that a knowledgeable office might shut you down as you are driving a bus that is still painted/marked in their states school bus paint/livery/markings which is against their state laws.
In my opinion the odd's of this happening with a school bus is about like the odds of winning the lottery UNLESS you drive the same road in Florida everyday where the same officer see's you as noted in a post above!
An example of this would be the the issue that has arisen in the vintage police car restoration world:
In Florida it is against the law to Operate or "Cause To Be Colored" that's what the law says meaning painting/repainting a vehicle in Florida Highway Patrol (FHP) paint scheme/livery/markings and drive/operate that vehicle on the streets in the State of Florida. ALL the State Patrol officers and most local yocals know this and will shut you down where you are at and tow the vehicle if you drive a vehicle in their state's FHP paint livery/markings. Same in California and a number of other states.
Say you own a vintage 1986 FHP Special Service Package Mustang that is restored in FHP colors with or without FHP markings and you live in Georgia. No biggie in GA. Drive where you want to go!
Just don't cross the state line into Florida UNLESS that restored FHP Mustang is on a trailer! It's OK if it's on a trailer, going to a show, hauling it through the state of Florida or whatever. Just don't drive the damn car in Florida!
Buy a surplus FHP trooper car in Florida at the state surplus auction that is still in FHP paint livery. You must trailer/ship the vehicle from the auction location. You cannot drive it out the gate! Auto dealer or individual it makes no difference.
Now I don't for a minute think most officer's in states with bus paint restrictions know they have em HOWEVER you never know and it just might be wise to be prepared if your bus is still in it's original livery and you have a bus registered in a state with restrictions OR your bus came from a state with paint/marking restrictions and you just might travel there one day in your bus with its original paint/markings!