Umm..that doesn't make sense. Mat or no mat, the slight height difference (vertical plane) will not alter the alignment which is an arc in the horizontal plane.
I think what people miss in this (for example some say an arc protractor is better) is that in this case, you are better able to allow for cantilever angle. Not every cantilever is an exact alignment to the cart/headshell. By aligning to the cantilever, you are perfecting the alignment of the diamond tip.
Picture this. The tip is on an arc and it follows that arc perfectly so you think you are aligned. But that TIP is held by a slightly off rod )the cantilever) and if you look at the tip, it is dead on (the diamond) to the cantilever. So while at the MACRO level, the whole assembly followed the arc, it did so with a slight lean on the diamond.
Hey, its not for everyone but I for one found that it took e that extra 5% better in alignment than a standard two point protractor.