Which datapack is the correct one, and why are there two? Genuinely wondering.

One is a true datapack. The other is a mod form of the datapack and will load in the mods folder. Use whichever one you want

This is the actual datapack and goes into datapack folder or is loaded by another mod:
https://www.curseforge.com/minecraft/texture-packs/repurposed-structures-friends-and-foes-datapack

This one is the mod form and will load from mods folder:
https://www.curseforge.com/minecraft/mc-mods/repurposed-structures-friends-and-foes-compat-mod

The mod form is what I am moving to for 1.20.4+ for all my datapacks