On the stock axle adjusters the right side has a smaller hole on the outside. The axle is put in from the left. As it comes out on the right the threads are all that comes through the outside adjuster hole. The hole is smaller to fit the threads.
If you put the adjusters on the opposite sides to put the axle in from the right, the mark one the adjuster you use to line up the wheel will be on the bottom. The right side adjuster only has one mark.
Drilling out the hole isn't the best thing to do. If you are using a hard tail with too thin an axle plate then washers to fill the gaps would be better, adding another layer of steel to the axle plates to get them as thick as stock will even be better.
Getting the people that build hardtails to use the right thickness of plate to start with would even be better.
Leo