Using a classical example, the Lorenz-63 model, an original stochastic framework is applied to represent large-scale geophysical flow dynamics. Rigorously derived from a reformulated material derivative, the proposed framework encompasses several meaningful mechanisms to model geophysical flows. The slightly compressible set-up, as treated in the Boussinesq approximation, yields a stochastic transport equation for the density and other related thermodynamical variables. Coupled to the momentum equation through a forcing term, the resulting stochastic Lorenz-63 model is derived consistently. Based on such a reformulated model, the pertinence of this large-scale stochastic approach is demonstrated over classical eddy-viscosity based large-scale representations.