MSET is a vulnerability of System Settings v4.x but it has been found out that you can downgrade System Settings on newer firmware versions and in the New 3DS as well.
Once you downgrade System Settings, you can use the MSET exploit without ever needing Cubic Ninja or OOT3D, but you need it once to downgrade System Settings.
NVRAM is what causes the exploit on System Settings v4.x. On an old 3DS, it resets whenever you play a DS games, however, it seems there is a way to keep it on New 3DS.
Even if it resets, you can use a DS flashcard or Cubic Ninja or OOT3D to reinstall the NVRAM.
Before you downgrade System Settings, make sure you have a NAND backup. If you downgrade System Settings, you can't:
- use Super Stable 3D settings
- format
- upgrade (maybe?)
But you can keep the new System Settings on emuNAND, so you can do all these things.
The downgrade is permanent unless you restore the original System Settings manually, so you won't need Cubic Ninja or OOT3D anymore.