On my printer, circular holes are consistently undersized even when the outside dimensions of the part are close.
For example, a 6 mm modeled hole ends up around 5.6–5.7 mm depending on orientation. I can compensate in CAD, but I would rather understand what is normal first.
Is the usual approach to calibrate extrusion/flow, verify dimensional accuracy, then use a small hole compensation value in the slicer or model?