The next check would be a compression test to see if this engine isn't damaged beyond affordable repair. If the engine passes this test then it would be time to install a thermostat and do a cooling system pressure test.
I suspect the sequence of events is the following:
The bike has developed some non-battery-related fault which prevents it from starting but doesn't prevent the starter motor from running.
You tried to start the bike with a good battery for 30 seconds. The current it takes to rotate the starter motor is very high. That current over 30 seconds heats all ...