Hi,
The heat ballast would hold true even for the substrateless method as there is still a substrate most of the time it just is not in direct contact with the egg.
Also, while the eggs need for air is not a huge amount by mammalian standards, it does still exist so if the box was small there would be less oxygen available - if you used a good seal this would be especially true.
So I think it would be perfectly possible to go too small with the egg boxes.
dr del
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