Magnetic quantum oscillations (MQO) are traditionally applied to investigate the electronic structure of metals. In layered quasi-two-dimensional (Q2D) materials the MQO have several qualitative features giving additional useful information, provided their theoretical description is developed. Within the framework of the Kubo formula and the self-consistent Born approximation, we reconsider the phase of beats in the amplitude of Shubnikov oscillations of interlayer conductivity in Q2D metals. We show that the phase shift of beats of the Shubnikov (conductivity) oscillations relative to the de Haas - van Alphen (magnetization) oscillations is larger than expected previously and, under certain conditions, can reach the value of π/2, as observed experimentally. We explain the phase inversion of MQO during the 3D - 2D crossover and predict the decrease of relative MQO amplitude of interlayer magnetoresistance in a strong magnetic field, larger than the beat frequency.