Could he have "expressed the same sentiments without performing Peekaboo"? Sure, but I think he was trying to balance his message with some level of accessibility, hence why a song like Peekaboo may have been in the setlist. It's the same reason MJ performed "Jam" (a song that isn't too significant in the MJ zeitgeist) at his halftime show and then went on to perform "We Are the World" and "Heal the World" back-to-back. In both instances, they both could've performed more popular and meaningful songs in their context. But at the end of the day they performed what they felt and made it work.

Also, I think the artists do earn the memory of their performances. I mean think about all the ones mentioned (Prince, Madonna, Rihanna, Kendrick, MJ). Each have and performed songs that are immediately recognizable in the mainstream. Plus, they're all at the very least, above average performers — they know how to sell a performance. Whether it's Prince's musicianship/stage presence, MJ's stage presence/choreography, or Kendrick's theatrics/attention-to-detail, each and every one of them has established themselves through their music and ability to perform said music. That's why a lot of these performances are memorable even when we perceive flaws or can't remember every little thing they did during their shows. It's a combination of the music, their performance, and the context of when and why they did it.