In a word, branding.
Back in the 90s the X-Men were the flagship Marvel title. Highest profile, highest selling, all that jazz. So when they tried to do a high profile Namor relaunch by John Byrne they stuck a big old "MARVEL'S First Mutant" on the cover to try and boost sales. Mutants sold, so now Namor was a mutant, deal with it.
These days mutants aren't as hot a brand, but the in-universe designation has stuck around. Much like how the effects of the current inhuman rebranding is going to linger for a long time.