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The scope of this paper is to compare two different approaches for solving the Wheeler-DeWitt (WDW) equation in the presence of homogeneous matter (inflaton) and perturbations around it. The standard Born-Oppenheimer (BO) decomposition, which consists of factorizing out the gravitational wave function and then defining the flow of the time through it, and a more general BO decomposition where the whole minisuperspace wave function is factorized out. The two approaches are compared, for simplicity, in the case of a minimally coupled inflaton with a flat potential. The consistency of the latter decomposition is checked against the former by comparing the resulting perturbation (Mukhanov-Sasaki) equations. Finally a few solutions to the homogeneous WDW not suitable for the traditional BO treatment are presented and the corresponding Mukhanov-Sasaki equations are evaluated.