We study the implications of a noncommutative geometry of the minisuperspace variables for the FRW universe with a conformally coupled scalar field. The investigation is carried out by means of a comparative study of the universe evolution in four different scenarios: classical commutative, classical noncommutative, quantum commutative, and quantum noncommutative, the last two employing the Bohmian formalism of quantum trajectories. The role of noncommutativity is discussed by drawing a parallel between its realizations in two possible frameworks for physical interpretation: the NC-frame, where it is manifest in the universe degrees of freedom, and in the C-frame, where it is manifest through theta-dependent terms in the Hamiltonian. As a result of our comparative analysis, we find that noncommutative geometry can remove singularities in the classical context for sufficiently large values of theta. Moreover, under special conditions, the classical noncommutative model can admit bouncing solutions characteristic of the commutative quantum FRW universe. In the quantum context, we find non-singular universe solutions containing bounces or being periodic in the quantum commutative model. When noncommutativity effects are turned on in the quantum scenario, they can introduce significant modifications that change the singular behavior of the universe solutions or that render them dynamical whenever they are static in the commutative case. The effects of noncommutativity are completely specified only when one of the frames for its realization is adopted as the physical one. Non-singular solutions in the NC-frame can be mapped into singular ones in the C-frame.