Orchid seed unlike corn or peas have no food source attached to them. In nature orchid seeds need to form a simbiotic relationship with a mycorrhizae bacteria. The bacteria provide the food for the growing protocorm. We need to provide a food source for the seed so we have agar. This is a nutrient gel that orchid seed will germinate and grow on. This agar also grows bacteria and molds very rapidly. This is why everything is done under sterile conditions.
This is also why you have to sterilize seed that has been exposed to the elements. If you use the green pod method the seed is still sealed inside the pod and is there for still sterile. Even though I use a glove box when I sow seed I still lose a small percentage of flasks to mold or bacteria. As for oxygen exchange I do not have any in my mother flasks. There is usually enough oxygen obtained when sowing the seed. I do have breathers in the replate flasks because the rapidly growing plants tend to use more.
Replating is also done in the glove box under sterile conditions. After all equipment has been sprayed to sterilize. (I use a 10% bleach solution) You are still taking sterile plants from one jar and moving them to another. With proper handeling (aseptic technique) there should be no contamination.