They are pretty thick. There's an extra, thinner piece of glass that came with the enlarger, which I really can't get my head around. Obviously this doesn't sit flat with the thicker top piece and neither does it solve the reflection problem. My enlarger is a Krokus 3 by the way.
I'd be very worried about scratches to the negative with aluminium, even if I was extra careful filing. Isn't this a problem with yours?