There is no standard way to tune a drum since the right way is the one that best suits the player or the piece of music that they are playing. With that said, there are a few practices that should be followed if you want to get a drum to perform at its best.
You need to keep in mind that pure pitches should be preferred since the sound produced is better and our ears prefer a pitch that we can sing to. If the head is fraught with dissonances caused by the tension rod, this can make the drum less distinguishable in a mix.
It is also very important to get quality drums since an instrument that features quality bearing edges, shells and hardware will not only perform better but will be easier to tune and it will stay at pitch for much longer. By following these two simple principles that hold true for most applications you can enjoy better results when playing your drums.