1) Good question. It seems that the two are actually very closely connected. Rashi explains that "Rofeh Chol Basar" praises Hash-m for creating in the person the ability to eliminate wastes through orifices in the body that heal (close) when the elimination is complete. "Mafli la'Asos" praises Hash-m for the miracle that man was created with holes (such as those to allow for elimination) but he still remains alive.

2) Another good question. The difference could be that earlier, when the Gemara said "Lo Liftach...," it was referring to someone who says, " Im Amus" -- " If I die." Here, though, one is praying that nothing bad should happen, which is indicated by the phraseology, " Pen Ishan ha'Maves" -- " Lest I die" (see Vilna Ga'on, Parshas Chayei Sarah (Bereishis 24:5)). Since a person must express his intention when he prays, he may explicitly mention his plea.