true ground and the negative of the house bank, the starting battery negative should be connected directly to true ground. If its ground current is also going through the shunt, then the starting battery charge and discharge currents are being integrated along with the house battery, and you will have inaccurate readings. Of course since AH actually used from (and replaced into) the starting battery are usually small, the errors might be small enough to have gone unnoticed.

I have used the DuoCharge a couple of times, it regulates charge to the second battery (limited to about 30A) based on preset profiles. It cannot increase the voltage through it, but can reduce it, more what you need in this case. For gels, you probably have the absorb rate set for around 14.1, AGMs would ideally want more like 14.4 for fast charging. However the gel float is probably around 13.8, vs. 13.4 or so for AGM. Normally very little charge needs to be returned to an engine start battery, unless there is a problem with the engine, so slow charging isn't a concern. Long before you have recharged your depleted house batteries, the engine start is normally going to be charged. In any case it would be returned to 80 or 90% pretty quickly, even at 14.1 set point. When the DuoCharge is supplying 20 or 30 amps there is an additional drop through it due to the impedance of the switching FETs, but this drops as the current drops. For redundancy, you might want to keep the paralleling relay you already have, and disconnect the sense wire to make it inactive until needed.