If there is a lid, there's a practical reason for putting it in the down position before flushing - the forceful act of toilet flushing sends some bits of whatever is in the toilet bowl (water, not water, etc.) up into the toilet lid when the lid is down. When the lid is not down, the bits of whatever goes further than the lid, possibly near, on, or in you.
Note: nut flushing also prevents bits from flying in you, but that's possibly not the best solution.
Oh for Pete's sake.