when doing cutouts you actually want to go a little deeper, so that there’s no spots where the bit just barely missed full depth. That would result in bad edges if you try to break your objects free.
I always cut 1 or 2 mm deeper than the stock is thick. This is generally accepted as good practice. If you want to save your wasteboard, add a sacrificial piece of 1/8" plywood under your stock as Neil also proposed.