Centralized trajectory optimization in the joint space of multiple robots allows access to a larger feasible space that can result in smoother trajectories, especially while planning in tight spaces. Unfortunately, it is often computationally intractable beyond a very small swarm size. In this paper, we propose Flow-Opt, a learning-based approach towards improving the computational tractability of centralized multi-robot trajectory optimization. Specifically, we reduce the problem to first learning a generative model to sample different candidate trajectories and then using a learned Safety-Filter(SF) to ensure fast inference-time constraint satisfaction. We propose a flow-matching model with a diffusion transformer (DiT) augmented with permutation invariant robot position and map encoders as the generative model. We develop a custom solver for our SF and equip it with a neural network that predicts context-specific initialization. The initialization network is trained in a self-supervised manner, taking advantage of the differentiability of the SF solver. We advance the state-of-the-art in the following respects. First, we show that we can generate trajectories of tens of robots in cluttered environments in a few tens of milliseconds. This is several times faster than existing centralized optimization approaches. Moreover, our approach also generates smoother trajectories orders of magnitude faster than competing baselines based on diffusion models. Second, each component of our approach can be batched, allowing us to solve a few tens of problem instances in a fraction of a second. We believe this is a first such result; no existing approach provides such capabilities. Finally, our approach can generate a diverse set of trajectories between a given set of start and goal locations, which can capture different collision-avoidance behaviors.