Real-time, text-promptable 4D reconstruction is indispensable for autonomous surgical interaction. Severe misalignment between semantic meaning and physical anatomy still persists, largely because existing solutions integrate Vision-Language Models into deformable fields via a rigid coupling scheme that tightly binds semantic features to geometric warping. In this paper, we propose DeGenseGS, Geometrically and Semantically Decoupled Surgical Scene Understanding in 4D Gaussian Splatting, a novel framework that independently models semantic evolution and geometric deformation. Specifically, we propose a HexPlane-based spatiotemporal entanglement module that uses shared kinematic latents to synchronize semantic mutations with scene dynamics, while explicitly disentangling semantic updates from geometric deformation. To further ensure robustness against reconstruction artifacts, we devise a Rasterization-Native Semantic Extraction mechanism that infers semantics from topologically continuous feature maps. Additionally, we incorporate an angular-aligned optimization strategy that conforms to the native hyperspherical latent space, thereby preventing semantic distortion. Extensive evaluations on the CholecSeg8k and EndoVis18 datasets demonstrate that DeGenseGS achieves state-of-the-art performance. Our framework yields enhanced geometric completeness and robust semantic-anatomic alignment, enabling spatially continuous segmentation despite drastic tissue deformation and topological transitions.
Effective multi-task learning for surgical scene understanding is fundamentally hindered by annotation granularity mismatch; temporal workflow tasks such as phase recognition, step recognition and anticipation benefit from dense frame-level supervision, whereas pixel-level spatial tasks including instrument segmentation and action recognition are only sparsely annotated on selected keyframes due to prohibitive labeling costs. This supervision imbalance undermines shared representation learning and limits joint optimization across heterogeneous surgical tasks. To address this, we propose Flow-guided Annotation for Robust Operating Scenes (FAROS), a flow-guided label interpolation framework, that combines zero-shot segmentation-based mask propagation with optical flow estimation to overcome the limitations of appearance-based propagation under challenging surgical conditions such as occlusion, smoke, and motion blur, generating temporally consistent dense pseudo labels from sparse keyframe annotations. The densified instrument masks and action labels are integrated into a unified Transformer-based multi-task framework that jointly learns surgical phase recognition, step recognition, anticipation, instrument segmentation, and action recognition, enabling balanced optimization between dense temporal supervision and sparse spatial supervision. The label interpolation quality of FAROS is first validated on the DAVIS 2017 benchmark under a sparse ground-truth protocol, confirming robust propagation beyond the surgical domain. Extensive experiments on GraSP, MISAW, and AutoLaparo benchmarks further demonstrate that FAROS significantly improves cross-task representation learning and enhances holistic surgical scene understanding performance across spatio-temporal tasks.