12.8v is fully charged for a 12v lead acid battery.
Or do you mean the alternator is only outputting 13,1v instead of 14v and a bit more?
What split charge relay is it that monitors the voltage? A relay does not do this. Do you mean a voltage sensitive relay? Which?
I cannot see why this is a problem. Does it not connect the cabin batteries?
The usual way is to charge the cabin batteries first, then connect the start battery as it needs less charge.
The SR2 is difficult for charging because the alternator runs off the cam shaft at half engine speed, you need a large pulley on the cam and the smallest pulley possible on the alternator.