In fusion 360 you could always adjust your "Stock to Leave". In your case make axial stock to leave -.0003 which should take an additional .0003 off assuming you have that much control..
Actually after I read your reply it downed on me that I could simply make the adjustment on my tool length setting in the list of tools on the machine.
The only tool I'm having the issue on is the shell mill.... and I'm guessing I just didn't get a real accurate measurement when I originally set up the tool. ( It's a bit challenging to measure the tool with 8 different cutters on it)
So your response got my mind going in the right direction!
Yep.... just bump the tool length offset +.0003" and you should be good! (which makes the machine think your tool length is .0003" shorter/higher/positive than you had measured it). That way the spindle (when it's on that tool number) will come down the additional .0003" for the cut.