You could do the direct line, and as you suspect, it would always charge the house bank and only charge the start bank if you place the switch to the "both" position.
But the first thing to do might be to check where exactly you're getting the voltage drop.* As oldfishboat points out, your drop does sound suspiciously like an isolator (I think he meant 0.7 volts, which is the standard drop of*a silicon diode).* If the drop is in the wire between the alternator and the selector, then changing the destination to the house bank won't change anything... you'll have the same drop there.* If the drop is in the path between the selector,electrical panels,*and the batteries, then you have a major problem in that circuit which really needs to be fixed.
If the drop is in the alternator to selector wire, you might want to beef that wire up ... these are frequently only #12 or #10 wires, and making them a #6 or a #4 will take care of the problem.* If that's not*practical to do, another option is to use a remote sensing regulator - you have the voltage regulator sense at the far end of the wire, so that the alternator output is made high enough to compensate for the drop across the wire.* There's a little danger here, however - if the sensing wire becomes disconnected from the alternator output, the regulator will force the alternator to full output.* The high end regulators that are designed for remote sensing (Balmar and such) will also limit the alternator voltage output to a resonable value if the sense line shows much lower voltage.
In any case, I'd suggest connecting a voltmeter between each point in the alternator-to-battery chain to try to determine where the voltage drop is happening, and plan a fix accordingly.*