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The rapid and reliable assembly of defect-free atom arrays is a fundamental challenge for scaling neutral atom quantum computing. While parallel rearrangement methods using spatial light modulators (SLMs) show promise, they suffer from significant computational overhead in two key sub-tasks: atom-site matching and hologram generation. In this paper, we propose a novel framework to address these bottlenecks and enhance the efficiency and fidelity of the assembly process. Our approach features a new optimization objective for atom-site matching that minimizes the longest movement path, and a Fourier U-Net model that integrates a Fourier Neural Operator (FNO) to enable real-time hologram generation. The model is trained in a fully unsupervised paradigm, leveraging the physical properties of holography to eliminate the need for costly ground-truth labels. Experimental results demonstrate our framework not only significantly outperforms state-of-the-art supervised CNNs but also achieves an inference speed orders of magnitude faster than traditional iterative algorithms, enabling real-time, dynamic atom rearrangement.