Scientific machine learning methods such as physics-informed neural networks (PINNs) increasingly rely on domain decomposition for better scalability while solving partial differential equations (PDEs) over complex geometries, yet the resulting composite loss comprising residual, boundary, and interface terms is highly susceptible to conflicting gradients that degrade training. This work bridges domain decomposition with projection-based gradient surgery to systematically mitigate such conflicts in 2D and 3D settings. We evaluate two existing projection-based algorithms, PCGrad and ConFIG, and identify their performance degradation in specific scenarios such as 3D domains with multiple overlapping interfaces. To address this limitation, we propose Norm-PCGrad, a normalized variant that achieves state-of-the-art accuracy across a range of 2D and 3D domain decomposition problems. Across the benchmarks considered, Norm-PCGrad consistently achieves the lowest relative $L_2$ error compared to training without gradient surgery as well as to existing algorithms such as PCGrad and ConFIG, while incurring negligible additional computational overhead. To improve computational efficiency of domain decomposition frameworks such as Extended PINN (XPINN), we propose replacing vanilla PINNs in selected subdomains with separable architectures such as Separable PINN (SPINN), reducing the computational cost from quadratic (or cubic) to linear. We additionally demonstrate that gradient surgery extends to physics-informed Kolmogorov-Arnold Networks (PIKANs), yielding substantial accuracy improvements for 3D domain decomposition and confirming the generality of the proposed approach across network architectures.

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