To answer some of your questions:
The jelly and air in the bottle are sterilized in a large pressure cooker. The work area ( table top, clean box and even the air in the room) are disinfected with a number of house hold chemicals such as rubbing alcohol & Lysol. Lastly the seeds are sterilized in diluted bleach and or hydrogen peroxide.
So far I have had very low rate of contamination, and the one that did get contaminated was a ceph root ( which I had guessed from the begging would not be sterile).