Webster’s 1913 defines “-ist” as: “A noun suffix denoting an agent, or doer, one who practices, a believer in.”
“Rapist” is derived from the noun form of “rape”. The verb form of “rape” is a recent innovation. (Well into the 20th century.) It’s the oddity, not “rapist.” We would talk of “The rape of the Sabine women,” not “the raping of the Sabine women,” and we would never say “The Romans raped the Sabine women.” (Ignoring that that example predates the more specific sense of sexual assault.)
Absent the verb form, “raper” would have been incorrect and strange sounding. We were already used to calling rapists “rapists” when we started using “rape” as a verb – and we continue to use rape as a noun. So why change the word to “raper?”
Rapist, bigamist, extortionist, terrorist – whatever. Any association you make with academics is coincidental. It’s just a noun thing.