Do I need to use/ interpret BMV-712 differently depending on whether battery is charged with shoreline or with alternator. I have the impression "fully charged " battery capacity is less with alternator so that 50% use drops battery voltage more when charged with alternator.
It does depend on your alternator and if this charges at a low voltage (old design at say 13.8V or Smart alternator with variable output voltage) then it may not get the batteries fully charged. However, properly set up, a BMV712 should say charged is charged but if the BMV712 settings are wrong then you can get 100% synchronisations early based.
A few details and we can help more, what voltage does shorepower absorption charge at, what voltage does the alternator charge at and give us a screenshot of your BMV712 settings. Also what type/size battery are you charging compared to the alternator output current.