The Queen is very obviously an individual that is separate from the Collective. In both the Confederation and prime timelines, she remains an individual with the same personality and desires despite having little or no Collective remaining. In "Endgame," she contradicts the Collective's decisions and issues them direct orders. When Picard calls the Queen out on destroying what remained of the Collective, she justifies it as an individual. She isn't literally a manifestation of the Collective, she's a person. This could not be any more clear.