Investigating the pathological mechanisms of developmental disorders including autism spectrum disorder is a challenge, because of the fact that the presented symptoms are a result of complex and dynamic factors such as genes, molecules, neural networks, cognitive behavior, environment, and developmental learning. In recent years, computational methods, including the Bayesian brain hypothesis, have been expected to provide a unified framework for understanding developmental disorders that explain the neurocognitive functions by describing the interactions between these factors. However, this approach is still limited because most studies have focused on cross-sectional task performance and lacked the perspectives of developmental learning (i.e., acquisitions of knowledge reflecting probabilistic and hierarchical structures in the environment). In this study, we proposed a new research method for understanding the mechanisms of the acquisition and its failures in hierarchical Bayesian representations using a state-of-the-art computational model, referred to as ``in silico neurodevelopment framework for atypical representation learning.'' Using the proposed framework, simple simulation experiments were conducted to examine whether manipulating the neural stochasticity and noise levels in external environments can lead to the abnormal acquisition of hierarchical Bayesian representation and reduced flexibility. Consequently, networks with normal neural stochasticity were able to acquire hierarchical representations that reflected the underlying probabilistic structures in the environment, including higher-order representation, and exhibited good flexibility. When the neural stochasticity was high, top-down generation using higher-order representation was impaired, although the flexibility did not differ from that of the normal settings. On the other hand, the networks with extremely low neural stochasticity demonstrated reduced flexibility and abnormal hierarchical representation. However, this altered acquisition of higher-order representation and flexibility was ameliorated by increasing the level of noises in external stimuli. These results demonstrated that our proposed method is useful for investigating developmental disorders with bridging multiple factors including the inherent characteristics of the neural dynamics, acquisitions of hierarchical representation, and external environment.