Recent progress in 3D generation has motivated growing interest in compact generative representations of complex 3D scenes. For native 3D Gaussian scenes, however, learning such representations remains challenging due to widely varying primitive counts, nonuniform spatial density, and differences in geometry and appearance even among spatially neighboring primitives. In this work, we introduce TriFold, a native 3D Gaussian VAE that encodes Gaussian scenes into a fixed-layout triplane latent and jointly reconstructs their geometry and appearance. The key insight is to impose structural regularity on the latent space while preserving the spatial adaptivity of the underlying Gaussians. During encoding, we use cell-wise learned queries to aggregate projected Gaussians into multiple slots per cell, reducing the information loss caused by single-feature pooling. During decoding, occupancy prediction identifies active regions, where query-based set prediction and candidate selection reconstruct local Gaussian sets with spatially varying primitive counts. Building on this representation, we train a latent flow-matching model for conditional scene-level 3DGS generation, enabling point-cloud-conditioned synthesis and single-image-conditioned amodal generation. Experiments demonstrate that TriFold achieves high-fidelity reconstruction and generation from a single image that provides only a partial observation of the scene, validating its effectiveness for native 3D Gaussian representation learning. https://fantasy-amap.github.io/TriFold

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