Angular momentum about the end of the rod will give you misleading results. For one the angular momentum of the incoming particle is zero about any point on its path. So after the impact, if you use this value, it means the resulting angular momentum is also going to be zero, which is inconsistent with reality.
What happens is that a certain amount of linear momentum is exchanged at the point of contact, and along the contact normal direction. This amount $J$ is called an impulse, and it is in units of $\text{[Newton second]}$. This exchange is just what is needed to translate and rotated the contacting bodies such that the contact conditions is met. In this case the particle has zero velocity after the impact.
So if the particle has initial velocity $v$, it carries momentum $p=m v$ which will be wholly transferred to the rod.
Now consider the rod, which as an impuse $J=m v$ applied to it on one end. This changes the momentum of the rod by $J$ and the angular momentum of the rod about the center of mass by $(\ell/2) J$. So the change in linear a rotational speed of the rod due to the impact is
$$ \begin{aligned}
\Delta v_{\rm rod} & = \tfrac{J}{M} = \tfrac{m}{M} v \\
\Delta \omega_{\rm rod} & = \frac{(\ell/2) J}{I} = \tfrac{\tfrac{\ell}{2} m v}{\tfrac{1}{12} M \ell^2} = \frac{6 m v}{M \ell}
\end{aligned} $$
To make a long story short, you need to state the equations of motion (result of impulse) at the center of mass, so when you are conserving angular momentum, it needs to be also specified at the center of mass.