Is there any way we can separate the charge controller out from the "converter"?

HOMER does not let you model the charge controller explicitly, so you have to combine it either with the converter or the battery. It is also not possible to model a system without an MPPT. The presence of the MPPT allows us to ignore the DC bus voltage, and thereby avoid the iteration required to determine the DC bus voltage. (Iteration is necessary because without an MPPT, the PV array output affects the battery voltage, but the battery voltage affects the PV array output in turn.)