I haven't used this recipe to make tortilla chips before, and I just use regular flour tortillas, although I'm sure corn tortillas are great for chips.
To make the chips easier to flip (and possibly solving the issue of having overdone and underdone chips), I just score the tortillas so that they're cut almost all the way through, but not quite. Then I put the whole thing in the pan, fry it on one side, and then use tongs to flip it over. When it is cool, I break the pieces apart. They don't always break evenly, but perfectly-triangular chips seem odd to me, anyhow.