I can't think of a good reason to have two separate 12V alternators. Charging a separate engine battery and a house battery bank can be handled in many less complex ways. Alternators are generally highly reliable, so a redundant system really isn't much benefit. If you will have a lead-acid battery for the engine, with your lithium house system, a battery-to-battery charger would be the way to go. That way you can program the B-to-B charger to match the charging profile needed by the other battery chemistry.
So... I would definitely go with the single large alternator. Having Beta do the install is a lot simpler, since the PTO on the engine will be all set up for the heavy loads of the large alternator with brackets and mounting points all using their standard engineering.
Charleston, SC, USA