The Brinkman penalisation method embeds boundary-value problems on complex domains into a simple computational box by modeling the solid region as a strongly dissipative medium, avoiding body-fitted mesh generation. We show that multi-symplectic Hamiltonian PDEs regularised by Brinkman-type penalisation retain a multi-conformal symplectic structure under a compatibility condition linking the symplectic matrix and the penalisation projection. This yields an exact local conservation law, under which the multi-symplectic two-form is conserved in the fluid region and decays exponentially inside the solid. The linear wave equation with Brinkman friction and Maxwell's equations with artificial Ohmic conductivity satisfy this condition, with explicit modified Hamiltonian densities. Building on this, we propose (i) structure-preserving numerical integrators via Strang splitting that satisfy a discrete conformal conservation law, and (ii) conformal symplectic neural operators that interleave exact dissipative flows with learnable multi-symplectic evolution operators, allowing geometry-dependent operator learning. Numerical experiments on wave and electromagnetic scattering demonstrate that our methods reproduce correct local energy budgets and avoid unphysical energy drift, providing a principled framework for physics-consistent scientific machine learning on complex domains.

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