The $M$-shell ionization in high-$Z$ atoms by low-energy light $_{1}^{1}\mathrm{H}$, $_{1}^{2}\mathrm{H}$, $_{2}^{3}\mathrm{He}$, and $_{2}^{4}\mathrm{He}$ ions have been studied systematically in the energy range $0.1--1.0\phantom{\rule{0.3em}{0ex}}\mathrm{MeV}∕\mathrm{amu}$ in order to verify the available theoretical approaches describing the $M$-shell ionization by charged particles in asymmetric collisions. The present low-energy data, combined with our earlier results reported for $M$-shell ionization by hydrogen and helium ions for higher energies, form a systematic experimental basis to test the theoretical predictions of $M$-shell ionization based on the plane-wave Born approximation (PWBA), the semiclassical approximation (SCA), and the binary-encounter approximation (BEA). In the PWBA based approaches the energy loss (E), Coulomb deflection (C), perturbed stationary state (PSS), and relativistic (R) effects were considered within the ECPSSR theory and its recent modification, called the ECUSAR theory, in which a description of the PSS effect was corrected to account for the united- and separated-atom (USA) electron binding energy limits. In the SCA calculations with relativistic wave functions the binding effect was included only in the limiting cases of separated-atom and united-atom limits. Possible contribution of the electron capture, multiple ionization, and recoil ionization to the $M$-shell vacancy production, which is dominated for light ions impact by direct single ionization process, are also discussed. The universal scaling of measured $M$-shell x-ray production and ionization cross sections was investigated in detail. Using the present data the isotopic effect has been studied by comparing the measured $M$-shell ionization cross-section ratios for equal-velocity hydrogen $_{1}^{1}\mathrm{H}$ and $_{1}^{2}\mathrm{H}$ as well as helium $_{2}^{3}\mathrm{He}$ and $_{2}^{4}\mathrm{He}$ isotopes. In addition, the ratios of measured ionization cross sections for $_{1}^{2}\mathrm{H}$ and $_{2}^{4}\mathrm{He}$ were used to investigate the role of the binding effect. The present results are of practical importance for the application of particle-induced x-ray emission technique in trace element studies.