I've wondered about this after once accidentally knocking the bilge pump switch from "off" to "auto" when putting the cover on.
On my boat the pump bypasses the isolator switch, so even with all other electrics off the pump will still work.
Of course bit of rain and next time I went to launch & turn the key nothing more than a dull clunk! very frustrating
I did think of getting a solar panel connected to the battery, but that involved being able to mount it securely (but removably) and there being more sun to charge the battery than rain to drain it, and leaving the console hatch open.
I'm just very careful to check the switch is off before leaving the boat, and leave the trunks down.