I think I found another game that requires a real MPU-401 in order to function, Linewars II.

Running the configuration (on a real DOS machine) with my SC55 and MT32 attached via SB16 gameport I can select either of them as output devices, or my SB or GUS, but on exiting the config menu and back into the game I get a message about the MPU-401 not responding to a reset/initialisation request.

I guess this can go down as needing a proper intelligent interface too.