Also, the Elachi/Vertians/Shroomies technically were introduced into the STO universe before appearing in Rise of the Federation, but only by a month, so it was probably too late to rename them anway.
It would've made absolutely no sense to give them a name like "Elachi," because they don't talk! They make no sound of any kind! I mean, they were introduced in an episode called "Silent Enemy," for Pete's sake. Silence is their defining trait. So how could they have a phonetic name for themselves? (For that matter, how can the Horta? And how do the names "Chewbacca" and "Wookiee" and "Kazhyyyk" exist when there are no K or B sounds in Wookie speech? These things always bug me.)
Logically, the only viable name for a species that can't pronounce human-style phonetics is a name given them by humans or some other species, either as a location-based demonym (such as "Vertian" from Gamma Vertis) or as a descriptive term of some sort (like "Groundskeepers" for Species 8472). I'm always careful of that distinction in my fiction, only giving alien-language names to species that can actually produce phonetic speech. So I'm glad nobody tried to compel me to use the Elachi name. I would've had to concoct some handwave that it was, like, the Andorian word for their star system or something.