Disconnect the wiring harness in the engine. Install a new fuse. Turn the switch. What happens? If it holds its engine related. If not it's a boat wiring problem.
I had a 2002 90 and it only had one 20 amp fuse internally. Nothing in the service manual about any 30 amp fuse. Another clue is that the fuse box you opened is part of the boat, not engine.
What in your boat uses and could draw high current? I don't know as I never had a 30 amp fuse in a boats fuse panel.
What's interesting, on the Merc. Commander 2000 and 3000 side bulkhead mounted common control boxes, power to the ON-OFF switch comes from the engine to operate the engine. If you had something wired to the switch, requiring a 30 amp fuse, the 20 amp fuse in the engine would blow first.
Only thing I can think of is that the boat has an auxiliary power relay to operate that "thing" that is driven by a 12v energizing coil that is wired to the ON position of the ignition switch. That would allow the load to blow the 30 amp fuse without blowing the 20 amp fuse in the engine that supplies power to the ignition switch.