From looking at the diagram draw I personally see no problem in how it wired other than that the two battery should be independently fused in case one shorts it will cause to other to discharge at an extreme high rate with a risk of explosion or fire. You even indicated that the alternator is a 3 phrase unit.

Many ride-on mowers use a similar setup except they only have one battery. Yes of there little to no drain when alternator output voltage is above the batteries voltage. Then as the alternator output voltage drops below the batteries voltage then they supply the addition power until drained to below the alternator output.

Last edited by AVB; 11/05/16 12:52 PM.