Where is the sound coming from? When you turn the igntiion key to ON at any time, the fuel pump will run for about 1.5 seconds then stop if the engine isn't running. This also flows fuel through the fuel return line to the tank. If the engine is hot and the fuel return line check valve is worn and not holding pressure, this can cause the vaporized fuel in the return line to bubble up through the fuel in the tank. This sounds like a bubbling, rumbling noise from the fuel tank under the rear seat. Is this what you are hearing?
As far as the flywheel still turning, how quickly are you returning to ON after shutting the engine off? The engine takes less than a second to stop turning from idle speed. Unless you are turning the key to START, the starter will not be engaging. To turn the key bcak to ON more quickly after stopping the engine would make em ask the question, "Why?"
It's pretty hard to misalign the starter and if the starter pinion were contacting the flywheel due to installing an incorrect starter, you would hear a grinding noise as long as the engine was turning until the interfering parts worn themselves some clearance. The interference would absorb some power since it takes energy to make noise, but to consume any appreciable amount of power would make a significant racket all the time the engine is running.