Thanks for the well written and detailed post.
To gain access to the ChargeMate Pro under the passenger seat...
After unbolting it as you said, were you able to move the seat without disconnecting it ?
I'm concerned with getting a fault code.
If you remove the seat suggest you pull the battery cable first. If you don't DO NOT start or switch on the ignition or you will have a fault code that will not clear when you reconnect, Been there done that. Fortunately I have access to up to date Snap-on scanner that I used to reset the fault. BTW Snap-on charges the mechanics over $1K for the software updates.
After looking at the CM40's spec, I think you're right. If the chassis battery is above 13.5, it's going to turn on. If it drops below 12.75, it will turn off. The level of the house battery isn't a factor. I guess the question is how well will a LiFePO4 charge at 13.5 vs > 14. Sounds like it's probably good enough for most.
I recently installed an Epoch LiFePO4 300Ah and can confirm that the CM charges it perfectly at around 35-40A, regardless of charge state. The battery’s own BMS obviously turns off charging when full. I posted a video on the process (https://youtu.be/mvSCNvk2hcA).