Spectral gradient methods, such as the Muon optimizer, modify gradient updates by preserving directional information while discarding scale, and have shown strong empirical performance in deep learning. We investigate the mechanisms underlying these gains through a dynamical analysis of a nonlinear phase retrieval model with anisotropic Gaussian inputs, equivalent to training a two-layer neural network with the quadratic activation and fixed second-layer weights. Focusing on a spiked covariance setting where the dominant variance direction is orthogonal to the signal, we show that gradient descent (GD) suffers from a variance-induced misalignment: during the early escaping stage, the high-variance but uninformative spike direction is multiplicatively amplified, degrading alignment with the true signal under strong anisotropy. In contrast, spectral gradient descent (SpecGD) removes this spike amplification effect, leading to stable alignment and accelerated noise contraction. Numerical experiments confirm the theory and show that these phenomena persist under broader anisotropic covariances.