As access to space and robotic autonomy capabilities move forward, there is simultaneously a growing interest in deploying large, complex space structures to provide new on-orbit capabilities. New space-borne observatories, large orbital outposts, and even futuristic on-orbit manufacturing will be enabled by robotic assembly of space structures using techniques like on-orbit additive manufacturing which can provide flexibility in constructing and even repairing complex hardware. However, the dynamics underlying the robotic assembly system during manipulation may operate under uncertainties (e.g. changing inertial properties). Thus, inertial estimation of the robotic assembler and the manipulated additively manufactured component must be considered during the structural assembly process. The contribution of this work is to address both the motion planning and control for robotic assembly with consideration of the inertial estimation of the combined free-flying robotic assembler and additively manufactured component system. Specifically, the Linear Quadratic Regulator Rapidly-Exploring Randomized Trees (LQR-RRT*) and dynamically feasible path smoothing are used to obtain obstacle-free trajectories for the system. Further, model learning is incorporated explicitly into the planning stages via approximation of the continuous system and accompanying reward of performing safe, objective-oriented motion. Remaining uncertainty can then be dealt with explicitly via robust tube model predictive control techniques. By obtaining controlled trajectories that consider both obstacle avoidance and learning of the inertial properties of the free-flyer and manipulated component system, the free-flyer rapidly considers and plans the construction of space structures with enhanced system knowledge. The approach naturally generalizes to repairing, refueling, and re-provisioning space structure components while providing optimal collision-free trajectories under e.g., inertial uncertainty.