A long standing problem in the modeling of non-Newtonian hydrodynamics is the availability of reliable and interpretable hydrodynamic models that faithfully encode the underlying micro-scale polymer dynamics. The main complication arises from the long polymer relaxation time, the complex molecular structure, and heterogeneous interaction. DeePN$^2$, a deep learning-based non-Newtonian hydrodynamic model, has been proposed and has shown some success in systematically passing the micro-scale structural mechanics information to the macro-scale hydrodynamics for suspensions with simple polymer conformation and bond potential. The model retains a multi-scaled nature by mapping the polymer configurations into a set of symmetry-preserving macro-scale features. The extended constitutive laws for these macro-scale features can be directly learned from the kinetics of their micro-scale counterparts. In this paper, we carry out further study of DeePN$^2$ using more complex micro-structural models. We show that DeePN$^2$ can faithfully capture the broadly overlooked viscoelastic differences arising from the specific molecular structural mechanics without human intervention.