It has been reported that the structural stability is significantly deteriorated under radio-frequency-ultrasonic perturbation at relatively low temperatures, e.g., near/below the glass transition temperature T(g), even for thermally stable metallic glasses. Here, we consider an underlying mechanism of the ultrasound-induced instability, i.e., crystallization, of a glass structure to grasp the nature of the glass-to-liquid transition of metallic glasses. Mechanical spectroscopy analysis indicates that the instability is caused by atomic motions resonant with the dynamic ultrasonic-strain field, i.e., atomic jumps associated with the beta relaxation that is usually observed for low frequencies of the order of 1 Hz at temperatures far below T(g). Such atomic motions at temperatures lower than the so-called kinetic freezing temperature T(g) originate from relatively weakly bonded (and/or low-density) regions in a nanoscale inhomogeneous microstructure of glass, which can be straightforwardly inferred from a partially crystallized microstructure obtained by annealing of a Pd-based metallic glass just below T(g) under ultrasonic perturbation. According to this nanoscale inhomogeneity concept, we can reasonably understand an intriguing characteristic feature of less-stable metallic glasses (fabricated only by rapid melt quenching) that the crystallization precedes the glass transition upon standard heating but the glass transition is observable at extremely high rates. Namely, in such less-stable metallic glasses, atomic motions are considerably active at some local regions even below the kinetic freezing temperature. Thus, the glass-to-crystal transition of less-stable metallic glasses is, in part, explained with the present nanoscale inhomogeneity concept.