I actually found a plugin that can fix this https://forums.rpgmakerweb.com/index.php?threads/accurate-playtime.104735/ It also fixes where running below 60 fps causes it to count slower. It seems to be a MV-only bug as RPG Maker MZ seems to have fixed this at least with the speed-up.
Also on part 3 of my video at 6:36, I mentioned about a minor spoiler where talking to Alyssa after gaining control of Syle would say Alyssa instead of Candidate which seems to be fixed in 0.7 since it shows the latter name. I remember playing 0.6 where it said Alyssa even though Syle hasn't learned what her name is at this point.