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... non quia coniurationis manifestum compererat, sed ut ferro grassaretur,...

In Cicero and Caesar, "non quod/quia" with the indicative accepts a reason as factual but denies its relevance. This would imply that Tacitus considers Seneca a conspirator, but Nero had him killed for other reasons. In Livy and Tacitus, "non quod/quia" is used simply for a rejected reason. This better fits the context.