We investigate the interplay between coherent effects characteristic of the propagation of linear waves, the non-linear effects due to interactions, and the quantum manifestations of classical chaos due to geometrical confinement, as they arise in the context of the transport of Bose-Einstein condensates. We specifically show that, extending standard methods for non-interacting systems, the body of the statistical distribution of intensities for scattering states solving the Gross-Pitaevskii equation is very well described by a local Gaussian ansatz with a position-dependent variance. We propose a semiclassical approach based on interfering classical paths to fix the single parameter describing the universal deviations from a global Gaussian distribution. Being tail effects, rare events like rogue waves characteristic of non-linear field equations do not affect our results.