Gon’s transformation isn’t really controversial at all. It actually subverts the very trope that your claiming people are upset about. It takes the entire “protagonist beats big bad with random powerup” and flips it on its head.

Instead of gon raging and getting some random, no drawbacks power up and killing meruem we instead see our lovable main character delve so deeply into his rage/grief that he loses all his potential and fighting ability and he never even meets the big bad guy of the arc.

This would be like if after using final getsuga tensho to kill Gin (not aizen!) ichigo then actually lost his powers and bleach just continued onwards without him.

Togashi isn’t subverting PIS. PIS and plot armor are present and defining in basically any work of fiction. Togashi is subverting the shonen tropes that rely wholly on plot armor and instead using character work (instead of PIS). Any matchup between an anime mc and a stronger villain will always have plot armor, whether it’s gon vs pitou or luffy vs crocodile we know the main character will always survive in a shounen.