The Bochner identity is a special case of the Raychaudhuri equation, obtained when the vector field is of gradient type.
Let $v$ be a vector field and let $a^\alpha=v^\alpha{}_{;\beta} v^\beta$ be its acceleration. The vector $v$ is neither normalized nor a gradient. The next identity
\begin{align}
\partial_v (v^\alpha{}_{;\alpha})&=v^\alpha{}_{;\alpha; \beta} v^\beta= v^\alpha{}_{;\beta; \alpha} v^\beta-R^\alpha{}_{\gamma \alpha \beta} v^\gamma v^\beta= (v^\alpha{}_{;\beta} v^\beta)_{; \alpha}-v^\alpha{}_{;\beta} v^\beta{}_{;\alpha}-Ric(v) \nonumber \\
&=a^\alpha{}_{;\alpha}-v_{\alpha;\beta} v^{\beta;\alpha}-Ric(v). \label{vod}
\end{align}
is used to derive both the Raychaudhuri equation (with acceleration and vorticity) and the Bochner equation. The connection with the former is easy, it is sufficient to assume $v$ normalized and split $v_{\alpha;\beta}$ in symmetric and antisymmetric parts. As for the connection with the latter we need to assume that $v$ is of gradient type.
So let $v_\alpha=\partial_\alpha u$ where $u$ is a function. We have
\begin{align*}
\theta&= u_{;\alpha}{}^{;\alpha},\\
a_\alpha&=u_{;\alpha;\beta} v^\beta =u_{;\beta;\alpha} v^\beta=v_{\beta; \alpha} v^\beta=\tfrac{1}{2} (v^\beta v_\beta)_{; \alpha}=\tfrac{1}{2} (u^{;\beta} u_{;\beta})_{; \alpha},\\
u_{;\alpha ;\beta}&=u_{;\beta;\alpha}.
\end{align*}
Thus our first equation in display becomes the Bochner identity
$$
(u_{;\alpha}{}^{;\alpha})_{;\beta} u^{;\beta}=\tfrac{1}{2} (u^{;\beta} u_{;\beta})_{; \alpha}{}^{;\alpha}-u_{;\alpha ;\beta} u^{;\alpha ;\beta} -Ric(u).
$$
In this derivation the normalization of $v$ was not used so it holds in any signature. In the Riemannian case we get the usual form
$$
g(\nabla u, \nabla \Delta u)= \tfrac{1}{2} \Delta( (\nabla u)^2)-(\textrm{Hess} \, u)^2-Ric(u).
$$
The geodesic vorticity-free Raychaudhuri equation is just a particular case because the vector field can be seen as the gradient of the distance function from a hypersurface to which the congruence is orthogonal. In this case the first term on the right-hand side, corresponding to the divergence of the acceleration, vanishes.
The Raychaudhuri equation in general relativity is often conveniently replaced by a Bochner type equation while dealing with hypersurface-orthogonal timelike geodesic congruences, in which case the vector field is the gradient of the Lorentzian distance from the spacelike hypersurface. The Raychaudhuri equation for lightlike geodesic congruences (used e.g. in Penrose's singularity theorem) does not admit this type of reformulation so the Raychaudhuri equation rather than the Bochner equation remains the tool of choice in general relativity.
In Riemannian geometry you can use the Bochner equation instead of the Raychaudhuri equation because in most cases you can see the unit vector field of the geodesic congruence as the gradient of a distance function, i.e. you don't have the problem of lightlike geodesic congruences for which the analog of such a function does not exist.