The look of the "fluke man" appears to be strongly based on a birth defect known as harlequin-type ichthyosis. Babies with this birth defect are born with extremely dry, cracked skin resembling scales or armored plating due to a defect in the gene that directs skin cell division, causing them to divide and grow far faster than the body's ability to shed them, also causing their mouth to be pulled into a wide, circular gape due to the tightly pulled skin, and giving them an "alien" appearance. In all except a tiny handful of cases, babies born with it don't live longer than a few days (a week at the most) because the skin cells divide so rapidly, their bodies simply can't consume and process enough nutrition to keep up with cellular division.
In the beginning, when Mulder is in the sewer to view the scene with the body, he gags and coughs from the smell. The local forensic cop said, "it's better if you don't breathe through your mouth;" is incorrect and the opposite of what one should do in such situations. One should not breath through the *nose* because odors and tastes are seriously restricted while the sinuses are closed off.