We present a systematic study of the phenomena of number squeezing and fragmentation for a repulsive Bose-Einstein condensate (BEC) in a three-dimensional double-well potential over a range of interaction strengths and barrier heights, including geometries that exhibit appreciable overlap in the one-body wave functions localized in the left and right wells. We compute the properties of the condensate with numerically exact, full-dimensional path-integral ground-state (PIGS) quantum Monte Carlo simulations and compare with results obtained from using two- and eight-mode truncated basis models. The truncated basis models are found to agree with the numerically exact PIGS simulations for weak interactions, but fail to correctly predict the amount of number squeezing and fragmentation exhibited by the PIGS simulations for strong interactions. We find that both number squeezing and fragmentation of the BEC show nonmonotonic behavior at large values of interaction strength a. The number squeezing shows a universal scaling with the product of number of particles and interaction strength (Na), but no such universal behavior is found for fragmentation. Detailed analysis shows that the introduction of repulsive interactions not only suppresses number fluctuations to enhance number squeezing, but can also enhance delocalization across wells and tunneling between wells, each of which may suppress number squeezing. This results in a dynamical competition whose resolution shows a complex dependence on all three physical parameters defining the system: interaction strength, number of particles, and barrier height.