Multimodal diffusion transformers (MM-DiTs) have emerged as the prevalent backbone for modern text-to-image generation systems. However, they exhibit critical alignment vulnerabilities, systematically manifesting severe stereotype biases even under benign prompts. This poses a significant risk of algorithmic discrimination in deployed systems. Since most existing mitigation strategies were tailored for legacy U-Net architectures, the precise remediation of these vulnerabilities in MM-DiTs remains a critical open challenge. In this work, we first investigate the root cause of this vulnerability via mechanistic analysis. We reveal that bias representations in MM-DiTs are not uniformly distributed across depth, but are mediated by a sparse set of layers functioning as internal semantic binding hubs. These hubs exhibit a stage-wise propagation driving bias manifestation: early hubs establish the structural templates susceptible to bias, middle hubs actively extract core stereotypical concepts from textual conditioning, and late hubs globally solidify these biases through visual self-attention. Leveraging these architectural insights, we propose FairFlow, an intrinsic, mechanism-guided mitigation framework. FairFlow acts as an internal regulator by employing sparse steering: it learns attribute-specific fair directions and injects them exclusively at the identified semantic hubs within a constrained inference window. Evaluations on FLUX.1-dev and Stable Diffusion~3 demonstrate that FairFlow effectively neutralizes these stereotypical vulnerabilities across gender, race, and intersectional settings, achieving an optimal fairness-fidelity balance. With near-zero inference overhead and robustness to complex prompts, FairFlow provides a lightweight and practical bias mitigation for large-scale deployed MM-DiT systems. Code and datasets will be publicly released upon acceptance.