"One item not considered with this licensing is if it there is an exclusivity clause in the agreement that prohibits the use of TMCC. "
This would potentially be illegal under anti-trust law , as an anti-competitive practice, should anyone want to litigate it. MTH could probably incorporate a legally defensible clause requiring Atlas use of PS3 in formerly MTH locos, but could not legally specify that a competitor's product could not be used at all. Atlas would be very foolish indeed to agree to restricting their use of other products down the road, of course, but we don't know and probably may never know the details of the contract.
I'm not a lawyer, of course .