As I recall, most FR4 stock is .062in thick. The thickness of the stock is not quite as important as to your specification of the stock.
One can have a PCB house plate copper onto the standard board stock to your specs, which might be more useful in your micro-strip design parameter selection.
To be fair, though, I am unfamiliar with the software tool you mentioned. I had to do the design the hard way and tweak as necessary.
Remark:
Read More: How to Choose the Right PCB Thickness?
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