Microstructure reconstruction is an important and emerging field of research and an essential foundation to improving inverse computational materials engineering (ICME). Much of the recent progress in the field is made based on generative adversarial networks (GANs). Although excellent results have been achieved throughout a variety of materials, challenges remain regarding the interpretability of the model's latent space as well as the applicability to extremely small data sets. The present work addresses these issues by introducing DA-VEGAN, a model with two central innovations. First, a $\beta$-variational autoencoder is incorporated into a hybrid GAN architecture that allows to penalize strong nonlinearities in the latent space by an additional parameter, $\beta$. Secondly, a custom differentiable data augmentation scheme is developed specifically for this architecture. The differentiability allows the model to learn from extremely small data sets without mode collapse or deteriorated sample quality. An extensive validation on a variety of structures demonstrates the potential of the method and future directions of investigation are discussed.