This is, I think, partly due to how the slicer routes the filament paths. I've had this problem moving between nozzle diameters and the only reason I could thin

This is, I think, partly due to how the slicer routes the filament paths. I've had this problem moving between nozzle diameters and the only reason I could think of was that it wasn't possible for the slicer to maintain both accurate hole diameters and the correct placement of filament relative to previous extrusions. The STL was identical, but the parts printed with a 0.8 mm nozzle were undersized and only the holes. My experience of this was with Cura and an Ultimaker S5. Generally you should always start printing loose holes and tightening them up as you go to see where the limit is. The simplest dimension to control is the perimeter. That can, for most parts, be perfectly accurate because there are no constraints on where the nozzle needs to avoid. However if you print a hole close to the edge of a part then the printer somehow has to lay down both an accurate edge to the hole while maintaining suitable separation from previously printed stuff. Essentially your design is quantised by the nozzle diameter within the perimeter of the part (I may be wrong here, but this seems like a simple explanation). You may have better results if you tune your part to the printer/nozzle you're using so that the slicer doesn't have to worry about leaving/filling gaps that are non-integer multiples of the nozzle size. In theory this shouldn't matter, because the hole perimeter can also be printed first, as it's an "outside" edge, but it doesn't always seem to work that way.