High-energy scattering processes, such as deep inelastic scattering (DIS) and quasielastic (QE) scattering provide a wealth of information about the structure of atomic nuclei. The remarkable discovery of the empirical linear relationship between the slope of the European Muon Collaboration (EMC) effect in DIS and the short-range-correlation (SRC) scaling factors $a_2$ in QE kinematics is naturally explained in terms of scale separation in effective field theory. This explanation has powerful consequences, allowing us to calculate and predict SRC scaling factors from ab initio low-energy nuclear theory. We present ab initio calculations of SRC scaling factors for a nucleus $A$ relative to the deuteron $a_2(A/d)$ and relative to $^3rm He$ $a_2(A/^3rm He)$ in light and medium-mass nuclei. Our framework further predicts that the EMC effect and SRC scaling factors have minimal or negligible isovector corrections.