Embodied trajectories, such as the executable motion sequences of robotic manipulators, underwater vehicles, and mobile robots, are a fundamental output of embodied AI. Modern generative models often treat them as a dense, monolithic signal generated point by point, fitting an intricate high-dimensional posterior while leaving the data's latent structure unmodeled, the same sample inefficiency long identified by the structured generative model literature. We argue that a compositional latent structure is a natural choice: many embodied tasks share recurring motion fragments that can be made explicit as a finite repertoire of reusable motion primitives, and compositional units naturally align with subtask boundaries to support task decomposition. Existing compositional generators, however, compose in a latent space and rely on post-hoc decoding to relate sampled units to actual trajectory segments. We instead compose directly in the physical trajectory space through a flow-matching framework with two coupled designs. Motion-Primitive Dictionary Learning equips each atom with a learnable length mask and binary starting indicators so the atom itself is the primitive, reused verbatim wherever it is placed. Structural Sparse Flow Matching with Geometric Constraints then generates a binary placement matrix using duration-aware tokenization and a differentiable geometric loss that enforces spatial continuity and temporal contiguity where adjacent primitives meet. On Open X-Embodiment and 3DMoTraj, the framework attains state-of-the-art accuracy and reduces the FDE/ADE ratio from 1.8 to 1.07, improving ADE by 19.2% and FDE by 21.0% over the strongest baseline.