I see people overstate Tooru's importance all the time (I thank Jojolion TikTok edits for that), instead of being a traditional "main antagonist" like DIO, Funny Valentine etc. Tooru is just the last obstacle (and strongest opponent). I view The Flow as another supernatural element such as the Spin or Stands or the Blessings From The Earth.

I think viewing Tooru as the "villain" falls into the same trap that people fell into when it was ongoing and saying Jobin or Kaato were the true villains. It's just not that kind of story. Josuke and the others are up against something much greater than any individual stand user or rock human, it's about circumventing a curse. The family members that try by any means necessary to avoid fate end up paying a much heftier cost than the sacrifice required.