In "A Comprehensive Russian Grammar", Wade states that in the past tense, the nominative case is used to indicate a permanent state, e.g.
"По профессии он был ботаник"
"By profession he was a botanist."
. . .while the instrumental case is chiefly used for temporary states, e.g.
"Во время войны я был офицером."
"During the war I was an officer."
But then proceeds to state that the instrumental case may also be used to denote permanent past states e.g.
"Она была сестрой Полевого"
"She was Polevoi's sister."
The explanation following this suggests that where you have two nouns (or noun and pronoun) linked by a form of 'to be', the more specific is nominative, the more general is instrumental. However, the reason I was looking this up was because I encountered a question sentence that read "Кем был Фома́?" where it seems like we're dealing with just one noun (Фома́) and the instrumental case is being applied to a question word, but also that this is about 'permanent state.'
When, in such a situation, would the instrumental be used and when--if ever--would the nominative be used?