I've managed to solve my issue of secrets not spawning at all, I've been testing on the steam version of the game and for some reason uploading the mod to the workshop and downloading it from there fixed it. I suspect that adding modded files to the vanilla folders directly doesn't work on that version and that instead they need to go in the installed_mods folder.
I have, however, run into another strange issue. I've made some other secrets as part of the same project that transform those who learn them, but despite people learning them in worldgen nothing seems to happen. It just gives the line and the person goes on to die of old age anyway.
Here's the new bugged secrets:
[INTERACTION:ANGELFORM]
[I_SOURCE:SECRET]
[IS_NAME:the form of a courageous angel]
[IS_SPHERE:COURAGE]
[IS_SECRET_GOAL:IMMORTALITY]
[IS_SECRET:SUPERNATURAL_LEARNING_POSSIBLE]
[I_SOURCE:SECRET]
[IS_NAME:the form of a beautiful angel]
[IS_SPHERE:BEAUTY]
[IS_SECRET_GOAL:IMMORTALITY]
[IS_SECRET:SUPERNATURAL_LEARNING_POSSIBLE]
[I_SOURCE:SECRET]
[IS_NAME:the form of a loving angel]
[IS_SPHERE:LOVE]
[IS_SECRET_GOAL:IMMORTALITY]
[IS_SECRET:SUPERNATURAL_LEARNING_POSSIBLE]
[I_SOURCE:SECRET]
[IS_NAME:the form of a prismatic angel]
[IS_SPHERE:RAINBOWS]
[IS_SECRET_GOAL:IMMORTALITY]
[IS_SECRET:SUPERNATURAL_LEARNING_POSSIBLE]
[I_TARGET:A:CREATURE]
[IT_LOCATION:CONTEXT_CREATURE]
[IT_REQUIRES:MORTAL]
[IT_REQUIRES:CAN_LEARN]
[IT_REQUIRES:CAN_SPEAK]
[IT_FORBIDDEN:SUPERNATURAL]
[I_EFFECT:ADD_SYNDROME]
[IE_TARGET:A]
[IE_IMMEDIATE]
IE_ARENA_NAME:angel
[SYNDROME]
[SYN_CONCENTRATION_ADDED:1000:0]
[IE_ARENA_NAME:ascendant angel]
[SYN_CLASS:ANGELFORM]
[CE_BODY_TRANSFORMATION:START:0]
[CE:FORBIDDEN_CREATURE_FLAG:SMALL_RACE]
[CE:FORBIDDEN_CREATURE_FLAG:HAS_ANY_FEATURE_BEAST]
[CE:CREATURE_FLAG:GENERATED]
[CE:CREATURE_FLAG:HAS_ANY_INTELLIGENT_LEARNS]
[CE:CREATURE_FLAG:HAS_ANY_INTELLIGENT_SPEAKS]
[CE:FORBIDDEN_CREATURE_CASTE_FLAG:DEMON]
[CE:FORBIDDEN_CREATURE_FLAG:HAS_ANY_NIGHT_CREATURE]
[CE:FORBIDDEN_CREATURE_FLAG:HAS_ANY_NIGHT_CREATURE_BOGEYMAN]
[CE:FORBIDDEN_CREATURE_FLAG:HAS_ANY_NIGHT_CREATURE_EXPERIMENTER]
[CE:FORBIDDEN_CREATURE_FLAG:HAS_ANY_NIGHT_CREATURE_NIGHTMARE]
[CE:FORBIDDEN_CREATURE_FLAG:HAS_ANY_NIGHT_CREATURE_HUNTER]
[CE:FORBIDDEN_CREATURE_CASTE_FLAG:CANNOT_BREATHE_AIR]
[CE:FORBIDDEN_CREATURE_CASTE_FLAG:IMMOBILE_LAND]
[CE:FORBIDDEN_CREATURE_CASTE_FLAG:MEGABEAST]
[CE:FORBIDDEN_CREATURE_CASTE_FLAG:SEMIMEGABEAST]
[CE:FORBIDDEN_CREATURE_CASTE_FLAG:TITAN]
[CE:FORBIDDEN_CREATURE_CASTE_FLAG:UNIQUE_DEMON]
[CE_SKILL_ROLL_ADJUST:PERC:200:PERC_ON:20:START:0]
[INTERACTION:DEMONFORM]
[I_SOURCE:SECRET]
[IS_NAME:the form of a depraved demon]
[IS_SPHERE:DEPRAVITY]
[IS_SECRET_GOAL:IMMORTALITY]
[IS_SECRET:SUPERNATURAL_LEARNING_POSSIBLE]
[I_SOURCE:SECRET]
[IS_NAME:the form of a blighted demon]
[IS_SPHERE:BLIGHT]
[IS_SECRET_GOAL:IMMORTALITY]
[IS_SECRET:SUPERNATURAL_LEARNING_POSSIBLE]
[I_SOURCE:SECRET]
[IS_NAME:the form of a diseased demon]
[IS_SPHERE:DISEASE]
[IS_SECRET_GOAL:IMMORTALITY]
[IS_SECRET:SUPERNATURAL_LEARNING_POSSIBLE]
[I_SOURCE:SECRET]
[IS_NAME:the form of a miserable demon]
[IS_SPHERE:MISERY]
[IS_SECRET_GOAL:IMMORTALITY]
[IS_SECRET:SUPERNATURAL_LEARNING_POSSIBLE]
[I_TARGET:A:CREATURE]
[IT_LOCATION:CONTEXT_CREATURE]
[IT_REQUIRES:MORTAL]
[IT_REQUIRES:CAN_LEARN]
[IT_REQUIRES:CAN_SPEAK]
[IT_FORBIDDEN:SUPERNATURAL]
[I_EFFECT:ADD_SYNDROME]
[IE_TARGET:A]
[IE_IMMEDIATE]
IE_ARENA_NAME:demon
[SYNDROME]
[SYN_CONCENTRATION_ADDED:1000:0]
[IE_ARENA_NAME:ascendant demon]
[SYN_CLASS:DEMONFORM]
[CE_BODY_TRANSFORMATION:START:0]
[CE:FORBIDDEN_CREATURE_FLAG:SMALL_RACE]
[CE:CREATURE_CASTE_FLAG:DEMON]
[CE:CREATURE_FLAG:HAS_ANY_INTELLIGENT_LEARNS]
[CE:CREATURE_FLAG:HAS_ANY_INTELLIGENT_SPEAKS]