This post made me realize the fact, thank you.
That explains why I see the Orion Charging current on the Victron Battery Shunt but NOT on the Simarine Solar+Alternator Shunt (my chargers, circled above in my diagram). The Orion XS are non-isolated and the negative terminal just serves to “balance” like you said.
As per your reasoning, I would have to add another shunt on each of the engine battery negatives. This is why when I had an isolated charger, I could see it correctly.
CASE CLOSED, Thank You.