I've seen people use transparent plastic containers to contain humidity whilst cloning, because evidentally the plant intakes moisture through the leaf(s) until it can create roots. Would there be any benefit of doing also this from seed, or is it best to let them beath?
Yes actually, the air is warmer in the under the plastic. But be aware you can over water and grow mold on the outside of the soil container. Try to make sure you open it frequently because you need the gas exchange
Generally causes more harm than good, plants need fresh carbon dioxide and the built up moisture droplets can cause sunspots, mildew and dampening off.
If you had a particularly warm, dry, or draughty environment, then having a cloche to shelter the seedling for the first few days wouldn't be foolish. Shouldn't be any need to cover it for more than a few days if at all, and it is important to protect it from strong direct light and let fresh air in to prevent it getting too humid.
Just open the vents at the top of the humidity dome. That should take care of the exchange of oxygen and co2