Hi Binkie
I must agree the two words you mention seem to be about equally obscure. Needless to say, I hadn't heard of either of them. But they appear in a few dictionaries, not just the 1913 Webster's, and it appears they are both occasionally used - mainly in medical writings - so they seem like fairly good candidates for our list.
The vast majority of our "rare" words are from a list prepared by somebody else, so I can't explain why some words are in and others out. But whenever a word is suggested, I'll add it if a reasonable case can be made out for it. The more the merrier!
So I'll add "phyma", and its alternate plural "phymata" for good measure.