Separating Alzheimer's Disease (AD), Parkinson's Disease (PD), and Healthy Controls (HC) using structural MRI remains challenging because disease signatures overlap and model performance can be strongly affected by data partitioning. We present HybridDualPathNet, a hybrid architecture combining EfficientNetV2-S for local features and Swin-Tiny for global context through a Cross-Fusion Attention (CFA) module. We evaluate the model in two experiments. First, on the Kaggle APD-3-Class dataset using an image-level split, the model achieves 98.25% accuracy. Second, on a combined Kaggle and Alzheimer's Disease Neuroimaging Initiative (ADNI) dataset containing 17,859 slices, we use a per-source split with patient-wise separation for ADNI subjects. In this setting, the model achieves 73.37% standard accuracy and a macro AUC of 0.880. Source-stratified evaluation reveals a substantial domain gap, with 91.2% accuracy on Kaggle test images and 59.2% on ADNI test images. Temperature scaling reduces expected calibration error from 0.130 to 0.015, while split-conformal prediction achieves 89.5% coverage. Saliency analyses using Grad-CAM++, Integrated Gradients, and occlusion indicate that model activations concentrate on brain tissue. These results highlight the importance of patient-level separation, cross-dataset evaluation, and uncertainty estimation when assessing MRI classification systems. The findings also show that strong performance on a single dataset does not necessarily translate to reliable generalization across imaging cohorts.

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