When the battery selector switch is in the #1 position for the starter battery I can still run everything from this battery, including all house items. Similarly, if I put the battery switch over to the #2 position for the house battery I can still run everything. Frankly, this confuses me. I always assumed the starter battery would just power the engine and nothing else, and that the house battery would then be used to power the electronics and house systems. I took the boat to a local dealer a few months ago to fix a leak in the hydraulic steering and while there I asked them to check the battery management. I specifically told them I wanted to assure the starter battery was only for the engine while the Group 27 house battery would be used to power everything else. When I picked up the boat they told me they had checked the configuration and that it was just the way I had said I wanted it. I know I should trust them, but I am still confused as to why I can power the house from the starter battery.
The motor home industry has, for many years, set up the start and house batteries as you state you expected them to be wired in your boat. My previous 1983 and my present 2008 motor homes (both class "A") have a wiring circuit where the start battery and house battery are not connected together when the engine is not running. The engine will be started only by the enging start battery. (they call it the "chassis battery). All house circuits are connected only to the "house battery". Thus, when a motorhome is parked, engine not running, there is no chance that the chassis battery will be run down by using interior circuits. The chassis battery is charged only when the engine is running. The house battery will power only the house circuits. It will be charged by a 12v converter (120vAC in, 12DC out) if "shore power" of 120vAC is available. This converter does not charge the chassis battery. The house battery will also be charged (along with the chassis battery)when the engine is running. All this is done without the user deciding on any switch positions. The element that allows this is a diode or relay circuit that allows power to flow into both batteries when the engine is running, but will not allow any power to flow from the chassis battery when engine is shut down. If everything is working as designed it is a fool proof system, and the user does not need to do anything toward power selection while motor homing.
I have never found the motorhome type circuit in the boats I've used. Most boats seem to have the circuit you describe, where the user decides which battery to use for what function. My CD is wired such that either or both batteries will power everything: (#1 or #2 or both).
So your original thinking and request of the local dealer is what the motor home industry uses as standard. Those involved in boating seem to have a better understanding of what is needed from our batteries and the decision is left up to us.