Maybe @bgwong can provide some input here, but I think that having a blank with any vial with the media in should be sufficient. Also, take a look at this thread Preventing wobbling of the glass vial for better OD measurements. I think using the 3D printed aligner + having a blank of a vial with media present at the start should be fine even if the vial is later switched out. We routinely switch vials out mid experiment to combat things like biofilm, and OD seems to be fine afterwards. I have not actually tested out how much effect changing the vial will have on a zero though.
Another thing to keep in mind is that temperature changes can effect the OD zero measurement (the diodes are temperature sensitive), so having the vials be at temperature before the zero is taken will also help to ensure a good measurement.