I’m not sure to understand everything (bad english), but normaly, if you don’t do nothing, with Slic3r or Cura or Simplify, with a 0.4 nozzle, you loose around 0.4mm in diameter for a vertical hole. That’s why there’s an option in Slic3r: “XY_compensation” since one year now. If you use an X mm nozzle, you must put ‘-X/2’ in this option, and then you’ve got a perfect size hole. External size will be the same for every nozzle, but not internal size. In general, I’m using Slic3r with XY_compensation for every ‘mechanical parts’, and Curaengine for every ‘artistic part'(faster and less internal crossing).
Try it with your big nozzles Ryan.