Q & A

WTF? The way you did Arcane Initiate means theurgy wizards get more spells than other wizards!!

Yes, this does result in +1 total spells granted at certain levels (less than half of the wizard levels, actually - 5 out of 11 - so only 5 total more free levelup spells known) than a non-Theurgy wizard. However:

• Theurgy wizards don't get a "savant" feature (spell-scroll-learning discount) like the other, vanilla BG3 subclasses do. Therefore it'll be a little harder and take longer for them to learn additional spells between levels. So 1 additional spell sometimes - just 5 total over the course of a whole game - is, in my opinion, not game-breaking.
• As I mentioned before, it would be really complicated and incompatibility-headache-inducing to implement this feature as written for 5e.
  For example: There would have to be 7 alternative spell lists [one for each domain] for every wizard level [so a total of 70 freaking spell lists, just for the base of this one feature], and some kind of BG3SE magic to ping and check, every time you learn a spell, to determine if you've added every domain spell to your spellbook yet, and - once you had - then dynamically switch over to one of 70 more, different spell lists for each future level up. Not only is that beyond me to create (I don't understand BG3SE very well), but 140 spell lists for one subclass is already double the lists that exist in vanilla for the entire wizard class, and that's just bloated and messy and an unnecessary overuse of game memory and processing for very little fun gained.
• If I granted the two domain spells at levels 3, 5, 7, and 9 and removed the spell choice completely at those levels... that's not fun for the player! Not getting to make any choices at all during 5 out of your 11 levelups? That's just a bummer. And if I'm going to make a mod, it's to increase the fun in a game, not take fun away.
• This subclas comes from D&D 5e "Unearthed Arcana" which was playtest material. And during playtesting of the Theurgy wizard, feedback consensus was that the subclass was weak and "railroaded"/prescriptive at lower levels, and then way too over-powered at higher levels. (That's why it never ended up published in any official WotC expansion books.)
  Therefore, in my opinion, giving the subclass an "extra" spell at some levels might balance out that feeling of lack of power in the early levels. (And since BG3 doesn't go beyond level 12, then the over-powered issue isn't an issue here because I won't be implementing those features, anyway.)

Why change anything for Arcane Acolyte? Why not just add the 1st-level Knowledge or Nature Domain benefit like the source material says to do for a level 6 theurgist?

Code limitation. That's why.

The 1st-level benefit of the Knowledge domain is to choose 2 expertise skills out of Arcana, History, Nature, or Religion. And for Nature, it's to choose 1 druid cantrip and choose 1 proficiency skill out of Animal Handling, Nature, or Survival. However, adding a selector (e.g. a spell or skill/expertise selector, like this) at level up has to be done in the progression - ergo, every level 6 theurgy wizard would then get this expertise/skill/cantrip selection and not just the Knowledge/Nature theurgist.

(There's probably a way to use BG3SE to add a skill selector to the subclass progression dynamically [based on a conditional check for what passive/status the character has], buuut I don't know how to do that, sooo.)