My pouches are still hot and wet at the end of the steam sterilization process. Is it OK to take them out of the sterilizer and set them on a towel?

No. Touching a wet sterilization pouch will contaminate it and then you will have to repackage it and resterilize it. Microbes can be easily transferred to instruments through wet packaging. Further, during the cooling process, air in the pouch contracts, sucking microbes through the paper. Leave them in the sterilizer until completely cool and dry. Placing them in a pouch rack which holds them on edge during the sterilization process will facilitate both sterilization and drying.