Relativistic isobar ($^{96}_{44}$Ru+$^{96}_{44}$Ru and $^{96}_{40}$Zr+$^{96}_{40}$Zr) collisions have revealed intricate differences in their nuclear size and shape, inspiring unconventional studies of nuclear structure using relativistic heavy ion collisions. In this study, we investigate the relative differences in the mean multiplicity ($R_{\mean{N_{\rm ch}}}$) and the second- ($R_{\epsilon_{2}}$) and third-order eccentricity ($R_{\epsilon_{3}}$) between isobar collisions using initial state Glauber models. It is found that initial fluctuations and nuclear deformations have negligible effects on $R_{\mean{N_{\rm ch}}}$ in most central collisions, while both are important for the $R_{\epsilon_{2}}$ and $R_{\epsilon_{3}}$, the degree of which is sensitive to the underlying nucleonic or sub-nucleonic degree of freedom. These features, compared to real data, may probe the particle production mechanism and the physics underlying nuclear structure.