In the past two decades, numerous relaxation or physical aging experiments of metallic glasses have revealed signatures of intermittent atomic-scale processes. Revealed via intensity cross-correlations from coherent scattering using X-ray photon correlation spectroscopy (XPCS), the observed abrupt changes in the time-domain of atomic motion does not fit the picture of gradual slowing down of relaxation times and their origin continues to remain unclear. Using a binary Lennard-Jones model glass subjected to microsecond-long isotherms, we show here that temporally and spatially heterogeneous atomic-cluster activity at different length-scales drive the emergence of highly non-monotonous intensity cross-correlations. The simulated XPCS experiments reveal a variety of time-dependent intensity-cross correlations that, depending on both the structural evolution and the q-space sampling, give detailed insights into the possible structural origins of intermittent aging measured with XPCS.