"Doctor....my arm hurts when I do this (raised up over my head)" Dr says... "Then dont do it!" Basically the same answer here. Not really necessary to shift gears while on muffs in any other position than trimmed level and straight.... and then just only to test the shifter if you are so inclined to think you need to test it out of water (I do all my shifter tests out of water statically, in other words with the engine not running.
If it shifts fine in the water (trimmed or turned as needed), then you are ok.
Also, depending on how much you are trimming the outdrive up or turning the wheel, the noise could be from your u-joints.