Background/Objectives: Rapid differentiation of ischemic and hemorrhagic stroke subtypes is vital for acute management. Although current deep learning models achieve high single-dataset accuracy, they suffer from "shortcut learning" and domain shift in external validation. This study proposes a hierarchical computer-aided diagnostic (CAD) system mimicking emergency triage. Methods: We introduce a 3-channel Radiology-Focused Preprocessing pipeline that feeds radiological Hounsfield Unit (HU) windows into Convolutional Neural Network (CNN) and Vision Transformer (ViT) backbones via asymmetric formats (.mat and .png). The architecture utilizes a novel joint cross-attention fusion network optimized by an Integrated Orthogonal-Focal Loss. Results: Our system achieved a 95.48% F1-score on the internal stroke dataset. However, multi-center external validation (AISD, BHSD, PhysioNet) using a Mask Anchor filter revealed a drop to the 58-62% range, exposing the "internal validation illusion" caused by hardware noise. Critically, models exhibited high precision (77%) but low sensitivity (57%) for ischemic stroke, proving prone to hemorrhage overdiagnosis. Multi-seed variance analysis demonstrated that the DenseNet201+ViT backbone yielded the lowest deviation (0.59) and highest stability, making it the most reliable architecture for real-world clinical integration. Conclusions: To overcome diagnostic challenges, future research must focus on multimodal architectures that combine 3D volumetric extraction with clinical data.

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