Maybe you can test this?
Personally I like the idea of retaining some Lead Acid capacity for a few reasons, but mainly as a fail safe. The system I am working on at the moment has lead acid and Lithium connected directly together. Ie no Cyrix unit in the system. As you correctly noted this does cause the Li battery to top-off the Pb at the end of a charge cycle, and the Pb does almost nothing on a discharge cycle until the Li reaches around 5% SOC. If you think about these two characteristics for a bit, you will realise that they are very good things. Li batteries don't like to remain at high SOC for too long (they won't), and the Pb batteries provide an extra buffer at low SOC to support the Lithium batteries as they near low Voltage disconnect.
If/when the Li batteries disconnect (for any of the reasons that can happen) the Pb batteries continue to power the boat systems with no outage.
Finally, as with your system, weight of the Pb batteries helps with the port side list of the 54.
Best regards, Dean