All the DC "neutrals" (often also referred to as "ground" in vehicles) in a boat are common - the separate battery banks share the DC neutral/ground. Only the hots are kept separate so there is no issue at all as far as electrical operation. It seems unusual to have a direct cable between the the two engine blocks but as far as function, there is no difference from the oem setup.
Since the batteries/banks are wired in parallel, using the parallel switch just increases the available amperage, not the nominal system voltage. IOW, parallel switching two 32V banks still gives you 32V but your available amp-hours doubles.
Of course, in reality there's hardly ever 32V in a 32V system, just as if there is seldom 12V in a 12V system. In both cases, if the batts are at the nominal voltage (32 or 12), the batts are at a very low charge level.