stealthrabbi, Default_Spirit_Levels needs to be active when a character is first recruited to function (when you name the girl or sprite). That's the point in time when character data is initialized, and so includes setting elemental levels (to 0 in vanilla, generally not 0 with Default_Spirit_Levels). If you hadn't had it enabled, and played past the point in the game where you name the girl and/or sprite, then enabled it (and repatched the ROM, etc.), that's one way for it to seemingly not work.
Echoherb, if you enabled Quality_of_Life\Gaias_Navel_Girl then yes, but it's not On by default.
hmsong, yeah, the two wall bosses share almost all of their code, it's practically just their respective desperation attacks that diverge.
Mr X, I'd looked at altering some of the logic concerning the side eyes, especially regarding mana, but didn't come up with anything that was worthwhile. Like all boss code, it's really unpleasant to work on, and I don't expect to revisit wall boss code any time soon. Lots of other bosses that still need an initial pass to try and iron out their worst wrinkles. The wall bosses will probably benefit as a side effect of collision code work I'm currently experimenting with, but it won't be focused on them in any way.
And on that topic (collision detection), despite the common complaints, this game's collision detection code is pretty solid (though messy and with separate implementations for almost every object interaction).
The only truly bad collision code is for basic projectiles (bow/javelin/boomerang); it's reliable, it just does a terrible job placing collision boxes since it disregards relative position offsets and uses square bounding boxes for the projectiles (e.g. the javelin is a massive 32x32 pixel square, not 32x8 like it looks like).
Boss skills that launch projectiles have more technically correct collision (they use the relative position offset), but can only collide every 5 frames, making them less reliable.
There are a few improperly defined collision rectangles, but that's defined per frame of animation, and most are good; I'm convinced the bulk of the complaints still stem from the lack of feedback on if a hit connected, and the delay before damage is applied, rather than any fault specifically in collision detection itself. There are some non-obvious situations where you and your target are at different heights (not like Z-distance off the ground, which does matter, but rarely comes into play, but instead ground height which is based on staircases usually) so that an attack isn't allowed to connect (I think Spring Beak is affected by this, where the design was where you need to be standing on one of the platforms for melee to hit, but where that's hard to accomplish due to positioning and only attacking in cardinal directions), but that accounts for very few situations.