Shouldn’t be a problem, but would require some firmware changes.
Using PF or PU motors would be quite a difference in the end, as they require different setups:
1) PF motors can be controlled directly with a motorshield attached to the MLC. Using the LEGO IR shield would also be an option.
2) PU motors could theoretically also be controlled with motorshields, or you would attach them to a PU hub. The MLC does not work with PU hubs, so these kind of changes would be more significant.
My five cents: it would be more economical to drive FX switches with a PF motor using the MLC with an additional motor shield. Maybe a nice little project for winter time.