Cura knows to offset the lines by half the nozzle width.  So that's not it.   However vertical holes are always printed too small.  Add around 0.4 or 0.5mm to every vertical hole diameter in CAD.   Also other things you can do to improve other dimensions: Make all printing speeds the same and around 35mm/sec or even 25mm/sec for super accurate.  Disable jerk and acceleration control (this will make ringing worse but will make dimensions more accurate).