Unmanned aerial vehicle (UAV) multimodal perception integrates visible (RGB), infrared (IR), synthetic aperture radar (SAR), and depth sensors for scene understanding under diverse conditions. However, differences in optics, resolution, and mounting often limit practical systems to global or image-center alignment. After tokenization, parallax, platform motion, and lens distortion can shift corresponding patch centers across modalities, weakening the spatial correspondence assumed by dense contrastive learning and cross-modal fusion. We propose GAAT (Geometry-Aware Alignment Transformer), an alignment-first pretrained model that estimates local correspondence reliability before cross-modal interaction. GAAT introduces syncPATC, which learns patch-center consistency under synchronized view transformations without correspondence annotations. It emits geometric priors, including token and query confidence, query centers, and sub-token offsets, that identify reliable local anchors across residual misalignment. Guided by these priors, MG-Sparse-MMA performs query-mediated sparse fusion over top-K_s reliable regions, replacing dense all-patch interaction with geometry-calibrated local updates. RA-QCGCL aligns pretraining supervision with this sparse query bottleneck through reliable patch-to-patch, patch-to-query, and query-to-query contrastive branches. We introduce UAVMeta and StateBench, which provide four acquisition-state scores derived from platform telemetry and image statistics: camera reliability, observation scale, viewpoint stability, and flight maneuver complexity. Extensive experiments across six downstream tasks demonstrate consistently superior transfer performance, establishing GAAT as a state-of-the-art multimodal foundation model for UAV perception. StateBench further enables a systematic diagnosis of real-world acquisition conditions.

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