I have a different model boat (Hunter 41DS), but my choice was to install the MPPT charge controller as close as possible where the combi charger/inverter has its connections.
On my boat, there are 3 4D batteries for the house bank. Two of which are underneath the nav station seat (starboard) and the 3rd below the salon slight to starboard. Whereas the actual combi unit lives slightly on the port side.
I am certainly not a marine electrician, but there was space for me to install the MPPT unit there, reasonable ventilation, and I figured by simply tying it in super-close (with a 40 amp breaker) to where the shore power charges and the inverter draws made the best since overall in regards to compliance and safety.
I ended up over clamping onto the existing (Magnum?) connections for the installation rather than installing a separate bus bar. I am sure there are those that may think this could be a bit substandard.
Anyway - as others have said, as close to your main battery bank bus-bar/terminals as you can is best approach. And make sure you fuse it or install a breaker between the MPPT and the batteries. And of course, a fuse/breaker near the panels where they feed the MPPT, especially if you are going with parallel panels and high amps.