Single-channel speech separation remains challenging for real-world deployment due to source permutation ambiguity, sampling variability of generative models, and the difficulty of processing long recordings with chunk-wise inference. We address these issues with a conditional flow-matching-based method that produces an ordered two-source output conditioned on the mixture. A frozen speaker encoder defines the source order during training and is reused at inference for biometric best-of-N candidate selection and chunk-level channel alignment. We evaluate separation quality on Libri2Mix benchmark using SI-SDR, PESQ, and ESTOI, and measure downstream impact using cpWER for automatic speech recognition and EER for speaker verification. The results show that the proposed Transformer U-Net variant is competitive with strong baselines in objective separation metrics and achieves the lowest downstream automatic speech recognition and speaker verification error rates in all evaluated settings.