This is correct.
The 3DO always resets when a disc is inserted. Games therefore expect a saved game in the NVRAM to be there. So set the NVRAM storage to "shared" and just play the game as normal.
The only reason for multi disc support in the emulator is to make the NVRAM shared. Not an useless feature but I've been busy with other things.
(note: I'm the maintainer of Opera)