I just checked a cheap set of dice in my 100-games-in-1 box, and the 1 dot is both wider and deeper than the 6 dots on the 6, the dots in the 2 also seem a bit deeper than the ones on the 6 side. I don't have any precise instrument to measure them, but it could be that the mold designer accounted for the removed (well.. not cast) material for the dice.

That's indeed a possibility, especially with modern manufacturing techniques allowing sufficiently-precise molds.