My primary instructor told me to use the "student pilot" call when I took my first solo xc (to Peoria!). I naively thought that if I told CMI when I got flight following, they would somehow pass that information to PIA. PIA tower then, assuming I knew what I was doing, sequenced me tight in front of a CRJ, which then had to go around. I'll never forget that. In my defense, I flew the plane normally, and she shouldn't have made me #1, but I'm hindsight there was an unspoken "I'm making you #1, keep it tight" that went right over the head of this "learner".
I think
@Racerx nailed the reasoning.... some puppy mill instrument student got called that and took offense because he's "NOT a 'student pilot'!". Because we no longer teach kids to deal with the slightest bit of being offended (that's called a micro- aggression now), we have to change the language.
As to whether ATC would understand "learner"....I bet it would confuse them, but you'd still get the "watch this guy, he might be an idiot" handling you're looking for