  We utilize a modified astrochemistry code which includes cosmic ray
attenuation in-situ to quantify the impact of different cosmic-ray models on
the CO-to-H$_2$ and CI-to-H$_2$ conversion factors, $X_{\rm CO}$ and $X_{\rm
CI}$, respectively. We consider the impact of cosmic rays accelerated by
accretion shocks, and show that clouds with star formation efficiencies greater
than 2\% have $X_{\rm CO} = (2.5 \pm 1)\times10^{20}$ cm$^{-2}$(K km
s$^{-1}$)$^{-1}$, consistent with Milky Way observations. We find that changing
the cosmic ray ionization rate from external sources from the canonical $\zeta
\approx 10^{-17}$ to $\zeta \approx 10^{-16}$ s$^{-1}$, which better represents
observations in diffuse gas, reduces $X_{\rm CO}$ by 0.2 dex for clusters with
surface densities below 3 g cm$^{-2}$. We show that embedded sources regulate
$X_{\rm CO}$ and decrease its variance across a wide range of surface densities
and star formation efficiencies. Our models reproduce the trends of a decreased
$X_{\rm CO}$ in extreme cosmic ray environments. $X_{\rm CI}$ has been proposed
as an alternative to $X_{\rm CO}$ due to its brightness at high redshifts. The
inclusion of internal cosmic ray sources leads to 1.2 dex dispersion in $X_{\rm
CI}$ ranging from $2\times10^{20} < X_{\rm CI} < 4\times10^{21}$ cm$^{-2}$ (K
km s$^{-1}$)$^{-1}$. We show that $X_{\rm CI}$ is highly sensitive to the
underlying cosmic ray model.
