Now that is an excellent question Don.Personally,for me,it depends what it is.Notches in a keel for the frames,I would aim for exact width of the frame but would leave a little meat for height adjustment.On Saint Philippe's frame mortices I go for exact depth but tweak the length with a sharp Scalpel.I try to minimise how much I allow for adjustment otherwise you can loose the sharp shape produced by the mill
I am an ex tool and dye maker and I have always cut smaller , measured and then cut to size. Measurements in your head even when I was young would suddenly change.
Play it safe cut the notches undersize, double check your measurement and finish cut.
It takes extra time but you are assured that its right.