The influence of the DC infrastructure on the control of power-storage flow in micro- and smart grids has gained attention recently, particularly in dynamic vehicle-to-grid charging applications. Principal effects include the potential loss of the charge–discharge synchronization and the subsequent impact on the control stabilization, the increased degradation in batteries’ health/life, and resultant power- and energy-efficiency losses. This paper proposes and tests a candidate solution to compensate for the infrastructure effects in a DC microgrid with a varying number of heterogeneous battery storage systems in the context of a multiagent neighbor-to-neighbor control scheme. Specifically, the scheme regulates the balance of the batteries’ load-demand participation, with adaptive compensation for unknown and/or time-varying DC infrastructure influences. Simulation and hardware-in-the-loop studies in realistic conditions demonstrate the improved precision of the charge–discharge synchronization and the enhanced balance of the output voltage under 24 h excessively continuous variations in the load demand. In addition, immediate real-time compensation for the DC infrastructure influence can be attained with no need for initial estimates of key unknown parameters. The results provide both the validation and verification of the proposals under real operational conditions and expectations, including the dynamic switching of the heterogeneous batteries’ connection (plug-and-play) and the variable infrastructure influences of different dynamically switched branches. Key observed metrics include an average reduced convergence time (0.66–13.366%), enhanced output-voltage balance (2.637–3.24%), power-consumption reduction (3.569–4.93%), and power-flow-balance enhancement (2.755–6.468%), which can be achieved for the proposed scheme over a baseline for the experiments in question.