Manifold alignment (MA) involves a set of techniques for learning shared representations across domains, yet many traditional MA methods are incapable of performing out-of-sample extension, limiting their real-world applicability. We propose a guided representation learning framework leveraging a geometry-regularized twin autoencoder (AE) architecture to enhance MA while enabling generalization to unseen data. Our method enforces structured cross-modal mappings to maintain geometric fidelity in learned embeddings. By incorporating a pre-trained alignment model and a multitask learning formulation, we improve cross-domain generalization and representation robustness while maintaining alignment fidelity. We evaluate our approach using several MA methods, showing improvements in embedding consistency, information preservation, and cross-domain transfer. Additionally, we apply our framework to Alzheimer's disease diagnosis, demonstrating its ability to integrate multi-modal patient data and enhance predictive accuracy in cases limited to a single domain by leveraging insights from the multi-modal problem.