Summary

Yosef Karo Translation:Shulchan Aruch — Orach Chaim 6…

There is a limit for the holes to be blocked and after this limit, one can't live "even one hour". This bracha is relevant to bathroom because the anus and penis are "holes", and intestines and abdomen are "cannular limbs". And furthermore, if one makes his needs more than needed and passes the "limit" he will die, therefore even the "cannular limbs" related to bathroom. "The healer of every body"- for the holes used to give off the wastes bring cure to the body. "And wonderful his deeds"- for the body is full of spirit like a balloon, and with little hole of needle the air goes.
Source: Wikisource

Yosef Karo Translation:Shulchan Aruch — Orach Chaim 6…

And the body has many holes and the spirit remains. Rem"a: And it is also possible to explain [the reason for saying the bracha] that it amazes to do what protects the spirit of man internally, and connects spiritual matters to physical matters, and this is all due to the fact that He is the healer of all living things, and so man is put on a path of health and his spirit is preserved internally.
Source: Wikisource

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