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When doing a backdoor Roth while married (whether filing separately or jointly) does the pro-rata rule apply to both partners' IRAs or is it by individual person?
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The question seems to be mixing unrelated concepts. As Opus 17 said, the pro-rata rule applies to the individual, so Form 8606 is an individual form no matter the individual's marital status or filing status. If both spouses make transactions that are reportable on Form 8606, a joint tax return will contain two Forms 8606, one for each individual.
MAGI, filing status and which spouses are covered by a workplace retirement plan determines the deductibility of the individual's traditional IRA contribution.
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