Q) When is the spell list for an auto-calc'd NPC built?
A) When the NPC is entry in a mod is saved in the CS. (It seems, but I'm still pretty unsure about when exactly it happens.)
Q) If true, is it just the CS that builds auto-calc'd NPCs and their spell lists upon saving? Does MWEdit do it as well? Enchanted editor or TESAME? (Almost certainly not, I imagine, for the lower-level editors.) If not, you need to make sure auto-calc'd NPCs are saved in the CS to ensure proper building, correct?
A) ?
Q) If so, what if we don't? What if we create an auto-calc'd entry in, say, Enchanted Editor, and it doesn't get properly built? Will the game fill in the blanks upon loading, or will it result in some sort of error/problem?
A) ?
Q) When does auto-calc'ing for other stats occur?
A) At the same time, when the NPC entry is saved. All auto-calc'd stats are built then.
Q) So how can we tell what spells got into an auto-calc'd NPC's spell list?
A) The spells that show in the the NPC's spell list are the ones that have been selected for that NPC by the Auto-calc mechanism.
Q) How can we tell how many times an auto-calc'd spell is being ref'd?
A) While the Object Window only shows non-auto-calc'd refs, the right-click/Info window will show both. So, for example, loading the Morrowind.esm master by itself and looking at the "spark" spell, it shows a count of 14 refs. But right-clicking and going to Info, it shows 41 refs. So the Info dialogue gives a reliable count of all auto-calc'd assignments of the spell to auto-calc'd NPCs (just subtract the number of assigned refs in the "Count" column on in the Object Window to get the actual number -- here, 41 minus 14, or 27).
Q) If you un-autocalc an NPC, save it without deleting his spell list, and re-autocalc him, will it erase the old spell list and rebuild it?
A) ? (I noticed a mention of this in, I believe, the WGI
readme -- something about un-autocalcing and then re-autocalcing NPCs
or something along those lines.)
Q) Is Spell Fix functionally sound for an average, non-modding-savvy player to use?
A) Not really, as it will either fail to have the desired effect (because the NPCs affected have not been re-saved), or it will have too much of an effect (leaving auto-calc'd spellcasters as their own chaff). This radical of a change needs to include a re-save of all NPCs.
Q) So, is there an easier way to have all NPCs re-autocalc'd than opening each entry and re-saving it?
A) ?
Actually, I think the auto-calc'd spell list is generated when the .esp/.esm are loaded in-game, and not saved (just like skills/attributes aren't saved). Since the NPC is auto-calc'd, I'm guessing that the game calculates everything for the NPC on loading according to the last plug-in's GMSTs. So the only way to know what will be on an auto-calc'd NPC's spell list (and their stats) is to load all the plug-ins that would affect auto-calculation by adding auto-calc'd spells, and/or changing the GMSTs governing auto-calculation.
Right-clicking a spell's info will show all the instances of the spell at the moment, though the 'count' in list view only includes instances where the actor is placed in the world, excluding levelled list actor entries.
So there really isn't a reason to re-calculate an auto-calc'd NPC as it's all automatic and done on-the-fly. Unless you just mean removing the auto-calc flag, in which case it's best done in the construction set so the attribute, skill, and spell entries will generate. Removing auto-calc will leave the NPC static, non-affected by the auto-calc system. I honestly don't know how the plug-in will react if an entry is flagged outside the construction set...
So basically, an auto-calc'd NPC is at the mercy of any plug-in that adds or affects auto-calculation in any way, while static NPCs are only affected if their assigned spells are changed to where they can no longer cast them (where auto-calc'd NPCs would re-calc their spell list for valid spells).
Hope this helps, kinda seems overly complicated and a bit convoluted.