For the PoP speedruns, when it says whole game above it does it mean completing PoP from the beginning to the end of PoP, or starting in PoP and going from there?

PoP% is in the category extensions. And yes, you start with a new file and it ends after completing PoP. Not to be confused with PoP, that you can find in the main categories

For clarity:

Path of Pain ILs, found under the "levels" tab here, only complete path of pain. Time begins on the load into the first room of PoP and ends on the load after the end cutscene. Your video evidence should not start in PoP as we need to see you enter the first room for accurate timing.

A different leaderboard exists for PoP%, where time begins on the load into King's Pass in a fresh save file and ends on the load after completing PoP. It can be found at https://www.speedrun.com/hkmemes?h=PoP-1.4.3.2_NMG&x=w20q1mzd-wlewrjxl.810pnzpl