One definition of the verb “fit” is “to experience or be affected with a seizure and especially an epileptic seizure” so the joke is the dad is interpreting the mom’s statement as the kid no longer having seizures. - Peter Griffin
I only know the phrase "throwing a fit", so I guess that "[he] doesn't fit" could be interpreted as "[he] doesn't have seizures". Bear in mind that I'm not a native English speaker. Tagging @iHUNTcriminals@lemm.ee in case they're interested as well.
I think it's trying to use the word "fit" as an "epileptic fit." As in, "he doesn't fit" in his clothes" = he doesn't have epileptic fits when wearing these clothes. I could be off the mark completely but that's the only explanation I can think of