Herein, we systematically explored how to tailor heterogeneity in the Ni-Nb-(Y, Gd) phase-separated metallic glasses (PSMGs) by carefully constructing a metastable miscibility gap and investigating its effect on the formation of heterogeneous shear band (SB) nucleation sites. The Ni60Nb40-x(Y, Gd)x PSMGs with either Nb-Y or Nb-Gd atomic pair (ΔHmix=+30 kJ/mol) showed hierarchically phase-separated microstructures at the nanoscale, which can be interpreted based on a metastable miscibility gap. Interestingly, statistical analysis of the initiation of plastic deformation via nanoindentation first pop-in analysis in these PSMGs reveals a unique trimodal distribution, unlike the bimodal distribution in monolithic MGs. This tendency arises from the formation of nanoscale phase boundaries as additional differentiated heterogeneous SB nucleation sites. The homogenously dispersed SB nucleation sites help hinder strain localization and SB propagation. In particular, a PSMG with a nanoscale interconnected structure exhibits homogeneous-like plastic deformation, where neither obvious pop-ins nor distinct surface shear steps are observed in the (nano-)indentation test. We believe this study's results provide an effective guideline for tuning correlative heterogeneity and related mechanical responses in PSMGs, highlighting the importance of tailoring microstructure even in MGs.