If you Select Core, then go for Loading Content, once you go for the N64 Folder, it crashes the System.
However, if you Select the Rom first, then go for the Cores, you get sent back to the Homebrew Menu. You try to run RA again, Atmosphere crashes again.
-But if you select Mupen64 Plus Next, it crashes the System.
Error Code: 2168-0001 (0x2a8)
EDIT: Found out later, RetroArch works best if it is run from a NSP/Card Game after holding R to load HBMenu, then running RA.