I don't mean to detract from your work on the new release, of course! Always good to see a new release

I'm just trying to understand the implications upon my somewhat hacky implementations
No worries, all questions very valid.
Do you mean the AI factors specific yields? Or, in non-DLL-understanding terms, looks at when the buildings produces any yield (or yield modifier?) and uses that to determine that the building is superior. This is helpful for Loyalty, if so, which adds to YieldModifiers but obviously the Loyalty yield itself would be unrecognized, so should if I understand correctly make the XP buildings a bit more valueable (as they produce Loyalty mods.)
Yes. All yields (for all yield types, including custom ones like Loyalty or Crime) are currently factored into a buildings value. Basically, the more yields a building has, the more valuable it is. Since all yields in the base game are 'positive' (i.e. beneficial), if I need to exclude 'crime' from this I can. Not a big deal to do.
But what if a building has a negative YieldModifier but which actually has a positive effect, which is the case with Crime and the Espionage buildings? I'd wager the AI would ignore this or, at worst, consider this a bad thing, in which case perhaps we can discuss a new flavour that helps the AI understand Crime a bit better (i.e. if is Crime high, it should pursue buildings with Crime flavour, with priority determined by the leader's value for that flavour). If this is possible (I don't know at all how the AI looks at flavours, so I don't know if adding new ones is easy, so forgive me if I'm considering too much), I can open an issue later.
Negative yield modifiers are not currently integrated, but I'll get to that before the next full release. Ones that 'positively' function with negative values (like plotculturecostmodifier, etc.) will be treated as positive functions.
If I need to write a custom crime function into the chooseproduction logic, I can. I have custom logic for CBP happiness buildings, so that shouldn't be too hard. Start a Github issue for what you need and we'll sort it out.
Somewhat related, does the AI factor flavours with a negative value? I know Health & Plague uses these to steer the AI away from Disease ridden Buildings which, flavour-wise, impact negatively upon Growth. I would probably do a similar thing with my Health & Disease, provided it would have an affect on the AI's decision-making.
Negative flavor values reduce an object's starting weight (sometimes to zero), which means that a zero'd value is passed into the 'sanity check' function (returning a zero). So yeah, negative flavors can and will reduce (or eliminate) a building/unit's possibility of creation.
The beta's system is still in development. The scaffolding is there, I just have more to do with it to make it better.
Here's a better breakdown of what is going on, for those who like crunchy behind-the-scenes stuff:
Prior to this beta, flavors defined everything for all 'decision' functionality in the DLL except for religious belief choice, specific unit selection for specific in-existence AI operations, and ideology selection (the latter only looked at happiness from policies, though). Flavors are defined by a few things at base: leader flavors and XML flavors. These base values were then inflated/deflated by: grand strategy flavors, economic ai strategies, city strategies, and military ai strategies.
Ilteroi and I had been chipping away at this for a while now (adding exceptions here, and 'if x, then y' functions there), but it was very fragmented and disorganized, especially in the 'chooseproduction' logic. So I've rationalized it by doing the following:
Chooseproduction:
For units, looks at geography, grand strategy, religious beliefs, war/no war, war type (land/sea), unit type, existence of certain economic/military/city strategies, need (i.e. no place to settle = no settlers) and city bonuses (free experience, free promotions, production modifiers, etc.).
For buildings, looks at geography, grand strategy, religious beliefs, war/no war, local terrain types, trade route options, tourism value at city, city/economic/military strategies, victory conditions, building yields/bonuses, and grandstrategy-specific bonuses (i.e. free votes or spaceship production).
For processes, looks at the yield value of the process and compares it to the city's deficient yields. Also, becomes available to puppets if you are in negative GPT and/or there's nothing else to build in the city.
For projects, looks at the grandstrategy value (i.e. apollo project), war value (nukes), and, for WC projects, the reward tiers (and personal value of said tiers to the player).
For Policies:
AI now looks at policies they've taken up to this point, as well as grand strategies (tying them to flavor types, but not flavor values). So policies with FLAVOR_OFFENSE are more valued by conquest grand strategies than others.
For Grandstrategies:
Now looks at policies (using same logic as policies themselves), national/local yields of yields that are specific to a VC (science for spaceship, production for conquest, culture for culture VC, etc.), religion, and some wonders (i.e. UN).
Again, the AI wasn't able to consider any of this before now. Flavors could, theoretically, push an AI in one direction, but it was largely listless (more like a sailing ship with flavors as the wind). Now they have a better idea of what stuff does and/or what they have 'acquired' over the game, so they're slightly more human in that regard. In other words, the AI isn't listing along, making each decision as if it is independent of all others – prior decisions now have a direct impact on future decisions.
I should note that I'm open to suggestions. If there's a part of 'human behavior' that I've missed, let me know.

G