I also wouldn't stack cut. When the material gets thick like that I tend to push to hard and the blade doesn't stay perpendicular to the table, so the top and bottom pieces wouldn't really be the same size.
I haven't really looked at the pattern, but I thought it would need the pieces to be the same. With some patterns it wouldn't matter as much the exact size or location of objects, or things could be sanded, so I might be tempted to stack.
For me it would also depend on the material being used, there are some materials that 1 inch total isn't too bad while others 1/2 inch is tough.