Positional encoding plays a pivotal role in determin?ing the extrapolation and generalization performance of wireless foundation models for channel state information (CSI) modeling, latent characterization, and task-specific prediction. However, existing CSI models inherit static or one-dimensional positional priors from natural language and vision architectures, which fundamentally misalign with the intrinsic physics of wireless channels by lacking explicit relative decay, collapsing the 3D spatio-temporal-frequency structure, and remaining scenario?rigid. This paper proposes Adaptive 3D-RoPE, a physics-aligned rotary positional encoding that establishes the structural corner?stone for wireless foundation models. The framework integrates a learnable, axis-decoupled 3D frequency bank to explicitly disentangle multi-dimensional phase dependencies, coupled with a lightweight channel-conditioned controller that dynamically modulates the prior via compact global CSI descriptors. This sample-adaptive mechanism transforms positional encoding from a static transformer component into a dynamic, coherence-aware inductive bias to resolve heterogeneous channel physics. Extensive experiments across 100 datasets demonstrate the superiority of the proposed scheme in both scale extrapolation and zero-shot generalization. Compared to the state-of-the-art, our method achieves up to a 10.7 dB reduction in normalized mean square error (NMSE) under 8 times antenna scale extrapolation. Given the same CSI input scales, our method can also improve zero-shot NMSE by 1.07 dB across unseen mobility scenarios and 0.90 dB in low-frequency-to-millimeter-wave tasks.