I don't understand batteries at all, but I remember being told that a battery doesn't 'see' any incoming charge if there is a load on the battery at the time. More accurately, the battery would only see a charge if the incoming current exceeded the outgoing current, and it would only see the 'marginal' current - the difference between the two. Presumably a shunt based ammeter would also only register the difference.
Which raises another point - the shunt based ammeter on our boat will happily tell me it's put many tens of Ah into the batteries over the winter, which makes sense as the boat is not being used, therefore no loads, so anything the solar panels sends down the cables to the batteries is a charge. Might a BMS 'remember', or take account of, these excess amps?
As I said, I don't understand batteries at all, so feel free to regard the above as a load of bollo if appropriate!