Hey Chris,
the buildbotics-derived Onefinity Controller DOES support tool change, however the code in the stock configuration does not work. You may use the Aiph5u’s tool change routine. You CAN have all tools in one g-code file.
Note that some CAM softwares like Carbide Create produce invalidated M6 Tx calls in their exported g-code files in order to make using another CNC control software difficult, but with a script you can change every instance of M6 commented out by a valid M6 Tx command.
See here for the g-code supported by the buildbotics-derived Onefinity Controller. It even supports a tool table.