This is just common sense (and electrical engineering!). The shunt develops a voltage across it proportional to current. The battery meter constantly measures this voltage, and knowing the proportional constant, integrates amps used over time, which is just amp hours. Now suppose we have two banks connected to the high side of the shunt. You use one bank until it is dead. The meter will accumulate the amps used over time. What should the meter read? Full (like the unused bank) or empty (like the used up bank)? If the banks are always paralleled on the positive side, then the readings will be accurate since. But if you have two banks used independently, you need two shunts. Otherwise the meter has no way of knowing which bank the current is draining from.

Two shunts would be advisable if you are using two house battery banks. But in the now normal setup of a house and an engine start battery, there isn't much need for a shunt on the engine start battery, since its use is momentary.

Can you post the diagram from Xantrex?

Edit: I should add that in the example described above, the meter will properly represent the energy state of the system a s whole, that is with one bank empty and one full it will read 1/2 full, which is correct for the system. But uninformative on each bank considered individually, and virtually useless if one bank is the engine start and the other the house.