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One of the main limitations in precision cluster cosmology arises from systematic errors and uncertainties in estimating cluster masses. Using the Mock-X pipeline, we produce synthetic X-ray images and derive cluster and galaxy group X-ray properties for a sample of over 30,000 simulated galaxy groups and clusters with $M_{\rm 500crit}$ between $10^{12}$ and $2\times 10^{15}$ M$_{\odot}$ in IllustrisTNG. We explore the similarities and differences between IllustrisTNG predictions of the Sunyaev-Zel'dovich and X-ray scaling relations with mass. We find a median hydrostatic mass bias $b = 0.125 \pm 0.003$ for $M_{\rm 500crit}$ $>10^{13}$ M$_{\odot}$. The bias increases to $b = 0.17 \pm 0.004$ when masses are derived from synthetic X-ray observations. We model how different underlying assumptions about the dependence of $Y_{\rm X}$ on halo mass can generate biases in the observed $Y_{\rm SZ} - M_{Y_{\rm X}}$ scaling relation. In particular, the simplifying assumption that $Y_{\rm X} - M_{\rm tot}$ is self-similar at all mass scales largely hides the break in $Y_{\rm SZ} - M_{\rm tot}$ and overestimates $Y_{\rm SZ}$ at galaxy and groups scales. We show that calibrating the $Y_{\rm X}-$mass proxy using a new model for a smoothly broken power law reproduces the true underlying $Y_{\rm SZ} - M_{\rm tot}$ scaling relation with high accuracy. Moreover, $M_{Y_{\rm X}}$ estimates calibrated with this method lead to $Y_{\rm SZ} - M_{Y_{\rm X}}$ predictions that are not biased by the presence of lower mass clusters or galaxy groups in the sample. Finally, we show that our smoothly broken power law model provides a robust way to derive the $Y_{\rm X}-$mass proxy, significantly reducing the level of mass bias for clusters, groups, and galaxies.