This might be splitting hairs, but thought it worth an ask. Encounter CR is based on the difficulty of an encounter as a whole - environmental factors, multiple opponents, etc.
If our villainess is CR 12 in the absence of such factors, but the entry contains information that would increase the CR of an encounter with her in certain conditions, would that result in a disqualification?
Basically, every villain has a lair, an ace in the hole, allies to call on, etc. But they don't always have access to them. Their "inherent" or "baseline" CR, so to speak, could be much different from their CR in a final showdown type situation.
No, the CR is for her as a component piece of an encounter - much like a creature CR. How she is used affects the encounter CR, not her personal CR. E.g. 1 modified goblin with "super bits" is CR 3, two modified goblins with "super bits" - they are both still CR 3 individually but the encounter is likely CR 4.
You will find in the bestiaries the CRs are for a single creature, with encounters taking that into account in the encounter design, rewards and tactics.
I am not worried about the tactics involving minions, confidents, bodyguards, etc - that would affect the encounter CR but not her personal CR. The tactics section should be reasonably generic, it is not an encounter design - that challenge comes later! I expect to see some paragraphs something along these lines, i.e. advice to the encounter designer/gm sort of thing...
"Assuming the PCs intend combat, when she is indoors and encountered alone, she uses her godlike bluff to confuse. She emits her psyhic call for help to her bodyguards to come quickly to her aide...
She is never encountered alone her in her throne room, a contingent of guards always present. She moves behind this wall of walking plate mail, muscle and loyalty and starts casting buff spells upon her minions....
Under an open sky, she immediately levitates to rain death down upon her attackers while silently summoning her nearby aides."
Note that in the second paragraph, I do not write an encounter design, there are no NPC stat blocks, no count of how many there are, just what she does to utilise them.
I hope that answers your question.
That clears it up, thank you!