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We calculate the Bose-Einstein condensate (BEC) occupation statistics vs. the interparticle interaction in a dilute gas with a nonuniform condensate in a box trap within the Bogoliubov approach. The results are compared against the previously found BEC-occupation statistics in (i) an ideal gas and (ii) a weakly interacting gas with a uniform condensate. In particular, we reveal and explicitly describe an appearance of a nontrivial transition from the ideal gas to the Thomas-Fermi regime. The results include finding the main regimes of the BEC statistics - the anomalous non-Gaussian thermally-dominated fluctuations and the Gaussian quantum-dominated fluctuations - as well as a crossover between them and their manifestations in a mesoscopic system. Remarkably, we show that the effect of the boundary conditions, imposed at the box trap, on the BEC fluctuations does not vanish in the thermodynamic limit of a macroscopic system even in the presence of the interparticle interactions. Finally, we discuss a challenging problem of an experimental verification of the theory of the BEC fluctuations addressing a much deeper level of the many-body statistical physics than usually studied quantities related to the mean condensate occupation.