I was testing Ultra Jungle biome raid dens in singleplayer and spawned in 100 raid dens with a redstone clock on command blocks changing the time and day to reset spawns. I noticed that the Tapu legendary pokemon do not spawn in these raid dens even after 1000's of raid resets.
Upon further investigation in the configs, it seems to be a syntax error where in "data\pixelmon\raids\raids.json" under jungle biome, the Tapu's are mislabeled. They have an ID of TapuKoko in files like legendary spawning and species, but in raids.json it is Tapu_Koko, this is the same for all the other Tapu pokemon.