you have two independent banks - one for engine start and one for house - and they are connected together at the high side of the current sensing shunt? That doesn't make sense to me.....how do you know what the state of charge of either is?

I think the problem of gels and AGMs in a parallel charging circuit would be early frying of the AGM due to high float voltage. The lower absorb would charge the AGM slower, but if used only for engine start that would not normally be an issue. You could use something like the Balmar DuoCharge to regulate the float voltage on the AGM.