Is there a difference in FDC or anything in the two layups? to make things easier to understand throw away stack thickness and look at the lams instead. yes both layups will have the same thickness but one has a parallel and the other has two .001 tapers.
layup #1
glass
veneer
.001
wedge
.001
veneer
glass
layup # 2
glass
veneer
.002
wedge
parallel
veneer
glass