Using a microscopic model for stochastic transport through a single quantum dot that is modified by the Coulomb interaction of environmental (weakly coupled) quantum dots, we derive generic properties of the full counting statistics for multi-stable Markovian transport systems. We study the temporal crossover from multi-modal to broad uni-modal distributions depending on the initial mixture, the long-term asymptotics and the divergence of the cumulants in the limit of a large number of transport branches. Our findings demonstrate that the counting statistics of a single resonant level may be used to probe background charge configurations.