Quick update . . .
While the system has been doing its charging thing while the boat lives on the mooring, I have noticed a few over voltage situations from the solar charging (via the DuoRacer controller). From what I can tell, the over voltages are brief, ( maybe a few seconds or less) and show up on the Xantrex Inverter as a fault. Not sure if it forced the LiFePO4 bank into protection mode (or not).
One of the geniuses on the DIY Solar forum suggested that the DuoRacer may be causing the over-voltage once the LiFePO4 batteries reach full charge and shut off their charging, and just for an instant, the DuoRacer has current with no place to go. (seems like a plausible explanation). . .
As a test, I have connected a BFC (big capacitor) to the circuit to absorb any rapid change in voltage. I'll see if it makes any difference over the next few weeks . . . i.e. if over voltage situations are remedied.
Keeping up with the changes, here is my latest diagram of the system for your viewing pleasure

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Summary of changes:
- SPST switch for DC-DC activation
- Removal of Alt/Batt isolator
- Capacitor for House Bank (LiFePO4)