A little late but I hope it helps. The SM64 EEPROM contains a number of bits used as boolean flags, you can read more about them
here.
Beating BitDW sets the flag "Have key to basement" in 0x0B. The "Castle Moat is drained" is a separate flag in 0x0A. So it should be possible to set the moat flag with GS etc. without having beaten BitDW.