The transfer from the superhumid atmosphere of the bags to the direr buoyant air of the pots i think is the main culprit of losses with the sealed bagging technique. The seedlings/cuttings are accustomed to a superhumid still environment and that is what I think kills most of them if they suddenly loose it. If that is your case, whether the bag is around the pot/germination bag is moot, the same shock will happen when you remove the bag.
What I do is I open the bag for 5-10 days prior to removing them, so they can get adjusted to a drier, more buoyant atmosphere. After that I remove it completely and let them get adjusted to being in open air in their geminating pots. After they are accustomed to that is when I move them to their permanent pots. A gradual transition is important I feel for very moisture-loving plants, like young ferns and other such plants. My first time gowing fern spores i opened the bag after the fronds had grown and potted them up in the window. I had 100% mortality of that batch. Granted, Ferns are different from cp's but now I treat all of the young mosture-loving plant seedlings this way and I have good sucess.
I never have much problems moving cuttings of drought-tolerant plants cold-turkey.
Er, thats my method.