As long as the openings are not horizontal, AFN is okay. Model the openings as windows with thin clear glass. Assign them as always open and on for natural ventilation. One bit that I'm unsure of is the window u-value. There is no window so I don't think energy should be transferred via this hole area in this mode. If the air were standing, then the conduction of heat in air would count, but air never stands and the AFN takes care of mass transfer into the zone. So really your glazing should be a perfect insulator to not double count heat transfer, because it's not there. So you may need to increase the insulation rating of the walls to either sides of the hole to make up the nonsensical heat transfer over glazing that does not exist. It depends on the amount of open area and the error in heat transfer.
Sorry for the long post. Your second option is to model the open to outdoors zones as simply not a zone and external. Walls, etc. are then simply shading surfaces.
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