A numerical investigation is undertaken on the development of linear disturbances in the rotating disk boundary layer, in which a time-periodic modulation is applied to the disk rotation rate. The model gives a prototypical example of a three-dimensional oscillatory boundary layer, by adding a Stokes layer to the von Kármán flow that develops on a steady disk. The study extends the Floquet analysis of Morgan et al. (J. Fluid Mech., vol. 925, 2021, A20), who showed that disk modulation stabilises the stationary convective instabilities found on the steady rotating disk. Using a radial homogeneous flow approximation, whereby the radial dependence of the basic state is ignored, disturbance development is simulated for several modulation settings, with flow conditions matched to both convective and absolute forms of linear instability. Disturbances excited via a stationary periodic wall forcing display behaviour consistent with that found using Floquet theory; time-periodic modulation stabilises the cross-flow instability by reducing the radial growth rate. In addition, convective and absolute instabilities, generated by an impulsive wall forcing, are both stabilised by the introduction of modulation to the disk rotation rate. Modulation establishes a significant reduction in both the temporal growth rate and the disturbance amplitude as it propagates away from the impulse origin. Moreover, greater stabilising control benefits are realised as the modulation amplitude increases.