yeah, they're entirely random alright. I tried to figure out in an emulator if there was any way of looking at the spot in memory that determines whether or not you play the "extra" bosses, but couldn't come up with anything. It's just random.
same goes for the elevators on Cyber-Lip, the Up/Down thing... you never know which direction is going to lead to the "extra" area.
it's pretty retarded that there's no way to guarantee these extra events to happen, since anyone going for a high score needs to play them, so they're entirely at the mercy of the game...