This is one of the points about modding cases, some people are more left handed or more right handed than others, more used to holding items like a case in a different way and of course some people have large hands and some have thin hands; some long fingers, some short.
When making holes for a case, you have to hold the product and put the holes where your fingers and thumbs will work naturally. For me, my middle finger on my right hand is entirely the right choice for the "Z" button; i've played on my iNto64 portable (as mentioned before, this N64 portable is up for a
raffle prize at the moment, so if you want to enter, please buy some tickets) and with games using "Z" like Super Mario, Conkers Bad Fur Day, etc and it really feels to be in the right place; positioned where my right middle finger rests, natural and works well.
If you make your own portable, there is no reason you shouldn't put the button placement anywhere you want it, of course.
