Changes to the Raid shiny rates, Raid HA rates, or Raid Gigantamax Factor rates in the in-game Pixelmon Config menu are reverted as soon as you exit the config menu. This makes it impossible to change the Shiny rates, Hidden Ability rates, and frequency of Gigantamax factors for Pokemon in Raids using the in-game config menu.
How to reproduce:
1) Enter a Pixelmon world.
2) Press the button that brings you to the Pixelmon Config
3) Click "Raids"
4) Make changes to Raid shiny rates, Raid HA rates, or Raid Gigantamax Factor rates.
5) Click "Done", then "Done" again
6) Reenter the Pixelmon Config.
7) Click "Raids". In the Raids menu, you should see that the Raid shiny rates, Raid HA rates, and Raid Gigantamax Factor rates are back to their defaults.
Tested using The Pixelmon Modpack in CurseForge.