In the new update, the generation of Neon and Alutine crystal caves seem to be little to none in the overworld, but they generate in menelaus??? I've also noticed that most dungeon parts don't generate nearly as much.

Please tweak the generation, thanks.

Something must have changed the generation which is not futurepack because I have zero Alutine or Neon Crystal Caves in Menelaus and if you want more Crystal Caves spawning you can change that in the config file. Did you change the config somehow?
Vers.: Futurepack-1.18.2-33.0.7544

1. there was no update recenlty (7544 is from may 28)
2. generation was not touched in month
3. there are configs for where and how often the spawn
4. do you play a modpack? maybe they changed that

If you can enter spectator mode and fly through your world that way you may have more luck finding things to reassure yourself they exist. When huge caves came out, I was in a world (of my making) where the little metal rooms all terminated in a cave and none reached the surface. ( well none near me, but i found them in spectator, then once i knew it wasn't a FP problem, I was fine)