Operator learning for partial differential equations (PDEs) on arbitrary geometries builds fast neural surrogates for large-scale simulation. While recent geometry-adaptive neural operators have made substantial progress, they are mainly designed for forward problems in which inputs and outputs share the same spatial domain. This limits their applicability for boundary value problems (BVPs) and inverse problems, where inputs and outputs may live on different domains. We introduce the Geometry-Adaptive Integral Autoencoder (GAIA), an operator learning model that encodes the domain boundary and the interior field distribution into geometry tokens, and conditions integral transform layers on these tokens via cross-attention, allowing the kernel to adapt locally to geometric features. This yields an architecture capable of learning solution operators for forward and inverse problems on arbitrary domains, solving each in a single pass at inference without per-domain optimization, iterative refinement, or graph construction. We evaluate GAIA on seven 2D and 3D benchmarks, four of which are new or substantially extended benchmarks for inverse problems and BVP: electrical impedance tomography, optical tomography, 3D Darcy flow on varying geometries, and a modified setting of the Poisson BVP on mechanical components benchmark (MCB). GAIA sets new state-of-the-art results on every inverse and BVP task, reducing median relative $L^2$ error by 64% on airfoil flow reconstruction and 22% on EIT relative to the next best amortized method, and outperforming all baselines on every shape category of MCB. On other forward problems, GAIA is competitive with specialized solvers while maintaining stable accuracy across point resolutions on which transformer-based baselines degrade.

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