Electromagnetic signal modeling is increasingly moving toward self-supervised pretraining on heterogeneous I/Q observations. However, an observed waveform is jointly shaped by signal generation, propagation environments, and acquisition processes, which mix reusable structural regularities with observation-specific variations. Existing methods usually pursue unified pretraining with reconstruction objectives on mixed observations. This heterogeneity creates two key mismatches for reconstruction pretraining: (1) appearance mismatch, induced by propagation-dependent waveform variations; and (2) temporal mismatch, induced by acquisition-dependent sampling coordinates. These mismatches make observation-specific appearances and sampling coordinates easier to reconstruct than stable signal structures, inducing observational shortcuts. We identify this failure mode as observation-biased pretraining. To address this, we propose Structural Pretraining with Time Alignment for heterogeneous EM signals. It mitigates temporal mismatch with RoPE-fs, which maps token positions to sampling-rate-normalized physical-time positions, and reduces reliance on appearance shortcuts by replacing waveform reconstruction with masked prediction of discrete structural units. These units are organized into atomic structural units and emergent structural units that capture variable-length compositional patterns beyond fixed patch boundaries. Across diverse EM benchmarks, our method improves both full-supervision and few-shot adaptation over existing EM pretraining baselines, showing that the learned representations better preserve structural consistency when observations drift in waveform appearance and temporal scale.

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