After an exchange with Corey and Fernando Licitra, here's what Corey had to say about the frog having to be submerged completely:
"My understanding was that it would get into the areas where the heaviest infestation of Chytrid would be (stomach/legs/areas that come in contact with the ground) and that some of these areas are where they absorb water from (drinking pads at the base of the legs/stomach), which would be how the drug got into the bloodstream and spread to the rest of the body - Chytrid is a systemic infection not just a topical one."
Fernando (Minhocao on this forum) is the one who his Phyllomedusa sauvagii lost an eye.
Any thoughts?