A quick fix is to prevent MUTC from changing the shuttle trains. In Mod Startup Settings, set the "MU Generation Blacklist" setting to "shuttle,electric_shuttle" (no quotes).
EDIT: Nevermind my previous edit, the remote interface does NOT add entities to behave as new shuttle trains. Adding that will require a lot of code in the shuttle trains mod. Adding them to the blacklist is the best I can do right now.