I like to think they reused that concept in Pikmin 1's "Bad Ending"
Where Olimars dead body is planted into the soil and reborn as an Olimar-Pikmin Hybrid.

From what I understand about mid-90s Miyamoto (for one I recall the dude would sometimes help promote games via Japanese Playboy magazine) I wonder if dark jokes like these or that one infamous Sattellaview comic were approved by him in an effort to "mature" Mario's image (supposedly he didn't like that someone added the "peace sign" hand gesture to Mario 64 due to believing it made Mario seem too childish), or if it's more a simple case of Nintendo management at the time legitimately just not looking over this stuff.

For the Miyamoto stuff btw from what I can tell he's mellowed out regarding the whole "annoyed that people viewed Mario as a character appealing to kids," for one he isn't averse to the peace sign being used (in Mario Odyssey, Mario alternates between the hand gestures he did in 64, Sunshine, and Galaxy).