Olivier - yes, you're right, the Victron system, as designed, doesn't just disconnect the faulty battery. The "load disconnect" signal from the Ve-BUS BMS triggers the BatteryProtect to disconnect all the loads that have been fed through the BP.

I agree that the safest approach is to run the genset when entering a marina. In my case, I rarely take by batteries below 40% SOC despite Victron telling me that I can take them down to 20% or even 0% with no damage. I guess I still have some lead in my head. :) One unintended side effect of being above 40% SOC is that the likelihood of the bow thruster causing a cell to drop below the low-voltage cutoff is very low. 

Dominique - I didn't have any challenges on the over voltage protection side.

Since I went full Victron, my Quattro and Skylla chargers are directly controlled by the Victron BMS, as is the Victron MPPT. At a cell over voltage/overheat event, the chargers are automatically turned off. As I wrote in an earlier post a few years back, I used a few relays to allow the BMS to control the "reg-on" wire of the Mastervolt Alpha Pro II alternator regulator, which safely turns off the alternator when cell voltage gets too high. Sounds like you solved the alternator problem using another BatteryProtect? Are you controlling the reg-on wire too?

As an aside, my Quattro will stop inverting in the event of a low cell voltage event. This could happen, for example, at a low SOC on unbalanced batteries if I'm running the scuba compressor and the washing machine is heating water and the admiral is busy listening to a podcast and turns on the boiler to make a cup of coffee.

My system is setup to protect its owners from their own mistakes, as I think all lithium systems should. 

--
Scott 
2007 A54 #69
SV Tengah
http://www.svtengah.com