I have this rule when I am working with stuff that needs close tolerances:
Do NOT adjust the geometry of the workpiece to suit the tool.
The geometry should always be the ideal size. If I am making .25 box joints those joints are drawn to .25 on both pieces no "tolerance" is built into them.
The reason is simple, modifying geometry leads to mistakes, offset the wrong way, etc. Plus if you go back to the job sometime in the future it is easy to forget that you changed the geometry to suit the tool. And, it is much easier to just click on the Edit Tool button, tweak the cutter and recalc the path. The original spec for the tool remains unchanged if the Edit button is used.
Low Profile CNC Router Vise