What you call the equation of geodesic deviation is called the Jacobi equation and the vector field $\xi$ is called the Jacobi field. The idea is the following.
A. Assume that you are given a space (smooth manifold) $M$ that has some Riemannian or pseudo-Riemannian metric.
B. Let $\gamma(t)$ be one fixed geodesic of that metric.
Definition. A Jacobi field $\xi(t)$ along the fixed geodesic $\gamma(t)$ is a vector field defined as follows:
1. let us assume that $\gamma(t)$ is included in a smooth one-parameter family of geodesics $\gamma(t, \sigma)$ such that $\gamma(t, 0) = \gamma(t)$. Smooth one-parameter family of geodesics means that the map $$\gamma \, : \, (t_1, t_2) \times (- \,\epsilon,\, \epsilon) \, \to \, M $$ is a smooth map such that for any fixed $\sigma \in (- \,\epsilon,\, \epsilon)$ the curve $\gamma(t, \sigma)$ is a geodesic of the space $M$.
2. Then the Jacobi vector field $\xi$ along $\gamma$ for the family of geodesics is
$$\xi(t) = \frac{\partial}{\partial \sigma} \, \gamma(t, \sigma)\Big|_{\sigma=0}
\,\,\,\,\,\text{ (i.e. first differentiate with respect to $\sigma$ and then plug $\sigma = 0$ )}$$
In other words, Jacobi vector fields along some fixed geodesic $\gamma$ describe in what directions and how much one should push $\gamma$ to turn it into a near-by geodesic. The Jacobi vector fields are very special because if you take an arbitrary vector field along $\gamma$ and use it to push $\gamma$ in the direction of that arbitrary field, the result may not be another geodesic but an arbitrary curve.
So the converse question arises: How can I tell whether a vector field $\xi(t)$ defined along a geodesic $\gamma(t)$ is a Jacobi vector field -- i.e. if for each $t$ I push $\gamma(t)$ along $\xi(t)$ would the result be another geodesic? Well, the answer is the Jacobi differential equation. In other words,
Theorem. A vector field $\xi(t)$ along the geodesic $\gamma(t)$ satisfies the Jacobi equation $$\frac{D^2}{dt^2}\xi + R\left(\xi, \frac{d\gamma}{dt}\right)\,\frac{d\gamma}{dt} = 0 $$ if and only if there is a smooth one parameter family of geodesics $\gamma(t, \sigma)$ sich that $\gamma(t, 0) = \gamma(t)$ and $$\xi(t) = \frac{\partial}{\partial \sigma} \, \gamma(t, \sigma)\Big|_{\sigma=0} $$
To justify this theorem you have to prove it in both directions, but I can sketch the direction which states that if $\xi(t)$ is a Jacobi field, then it must satisfy the Jacobi equation, i.e. deriving the Jacobi equation.
The Jacobi equation is simply the first variation of the geodesic equation. That is why the right hand side is equal to zero. Because the right hand side of the geodesic equation is zero. Here is what I mean: for each $\sigma$ the curve $\gamma(t, \sigma)$ is a geodesic. Then the geodesic equation says
$$\nabla_{\frac{\partial \gamma}{\partial t}(t, \sigma)} \,\frac{\partial \gamma}{\partial t}(t, \sigma) = 0 $$ Now, if you differentiate this geodesic equation with respect to $\sigma$ and set $\sigma = 0$ you get the Jacobi equation
$$\frac{D^2}{dt^2}\xi + R\left(\xi, \frac{d\gamma}{dt}\right)\,\frac{d\gamma}{dt} = 0 $$
Indeed, differentiating with respect to $\sigma$ means taking the covariant derivative with respect to $\sigma$, i.e.
$$\nabla_{\frac{\partial \gamma}{\partial \sigma}(t, \sigma)} \left( \nabla_{\frac{\partial \gamma}{\partial t}(t, \sigma)} \,\frac{\partial \gamma}{\partial t}(t, \sigma) \right) = 0$$
However, by the definition of the Riemann tensor
$$\nabla_{\frac{\partial \gamma}{\partial \sigma}(t, \sigma)} \nabla_{\frac{\partial \gamma}{\partial t}(t, \sigma)} =
\nabla_{\frac{\partial \gamma}{\partial t}(t, \sigma)} \nabla_{\frac{\partial \gamma}{\partial \sigma}(t, \sigma)} + R\left( \frac{\partial \gamma}{\partial \sigma}(t, \sigma), \, \frac{\partial \gamma}{\partial t}(t, \sigma) \right)$$ so
\begin{align}
0 =& \nabla_{\frac{\partial \gamma}{\partial \sigma}(t, \sigma)} \nabla_{\frac{\partial \gamma}{\partial t}(t, \sigma)} \,\frac{\partial \gamma}{\partial t}(t, \sigma) = \\
=& \nabla_{\frac{\partial \gamma}{\partial t}(t, \sigma)} \nabla_{\frac{\partial \gamma}{\partial \sigma}(t, \sigma)}\, \frac{\partial \gamma}{\partial t}(t, \sigma) + R\left( \frac{\partial \gamma}{\partial \sigma}(t, \sigma), \, \frac{\partial \gamma}{\partial t}(t, \sigma) \right) \frac{\partial \gamma}{\partial t}(t, \sigma) = \\
=& \nabla_{\frac{\partial \gamma}{\partial t}}\left( \nabla_{\frac{\partial \gamma}{\partial \sigma}}\, \frac{\partial \gamma}{\partial t}\right) + R\left( \frac{\partial \gamma}{\partial \sigma}, \, \frac{\partial \gamma}{\partial t} \right) \frac{\partial \gamma}{\partial t}
\end{align}
However, if by we come back to the interpretation of $\gamma$ as a two-parameter smooth map, as given in point 1 above, then
$$\frac{\partial \gamma}{\partial t}(t, \sigma) = \gamma_{*(t,\sigma)} \frac{\partial}{\partial t} \,\,\, \text{ and }\,\,\, \frac{\partial \gamma}{\partial \sigma}(t, \sigma) = \gamma_{*(t,\sigma)} \frac{\partial}{\partial \sigma}$$ where $\gamma_{*(t,\sigma)}$ is the derivative map (the tangent map) of the map $\gamma$ at the point $(t,\sigma)$. Based on the fact that there is no torsion of the covariant derivative, since it comes from a metric
\begin{align}
\nabla_{\frac{\partial \gamma}{\partial \sigma}}\, \frac{\partial \gamma}{\partial t} =&
\nabla_{\gamma_{*} \frac{\partial}{\partial \sigma}}\, \gamma_{*} \frac{\partial}{\partial t} = \nabla_{\gamma_{*} \frac{\partial}{\partial t}}\, \gamma_{*} \frac{\partial}{\partial \sigma} + \left[\gamma_{*} \frac{\partial}{\partial t}, \gamma_{*} \frac{\partial}{\partial \sigma}\right] = \\ =&
\nabla_{\gamma_{*} \frac{\partial}{\partial t}}\, \gamma_{*} \frac{\partial}{\partial \sigma} + \gamma_{*}\left[\frac{\partial}{\partial t}, \frac{\partial}{\partial \sigma}\right] =
\nabla_{\gamma_{*} \frac{\partial}{\partial t}}\, \gamma_{*} \frac{\partial}{\partial \sigma} + 0 \\ =& \nabla_{\frac{\partial \gamma}{\partial t}}\, \frac{\partial \gamma}{\partial \sigma}
\end{align}
So we continue the derivation of the Jacobi equation
\begin{align}
0 =& \nabla_{\frac{\partial \gamma}{\partial \sigma}(t, \sigma)} \nabla_{\frac{\partial \gamma}{\partial t}(t, \sigma)} \,\frac{\partial \gamma}{\partial t}(t, \sigma) = \\
=& \nabla_{\frac{\partial \gamma}{\partial t}(t, \sigma)} \nabla_{\frac{\partial \gamma}{\partial \sigma}(t, \sigma)}\, \frac{\partial \gamma}{\partial t}(t, \sigma) + R\left( \frac{\partial \gamma}{\partial \sigma}(t, \sigma), \, \frac{\partial \gamma}{\partial t}(t, \sigma) \right) \frac{\partial \gamma}{\partial t}(t, \sigma) = \\
=& \nabla_{\frac{\partial \gamma}{\partial t}}\left( \nabla_{\frac{\partial \gamma}{\partial \sigma}}\, \frac{\partial \gamma}{\partial t}\right) + R\left( \frac{\partial \gamma}{\partial \sigma}, \, \frac{\partial \gamma}{\partial t} \right) \frac{\partial \gamma}{\partial t} = \\
=& \nabla_{\frac{\partial \gamma}{\partial t}}\left( \nabla_{\frac{\partial \gamma}{\partial t}}\, \frac{\partial \gamma}{\partial \sigma}\right) + R\left( \frac{\partial \gamma}{\partial \sigma}, \, \frac{\partial \gamma}{\partial t} \right) \frac{\partial \gamma}{\partial t} = \\
=& \nabla_{\frac{\partial \gamma}{\partial t}(t, \sigma)}\left( \nabla_{\frac{\partial \gamma}{\partial t}(t, \sigma)}\, \frac{\partial \gamma}{\partial \sigma}(t, \sigma)\right) + R\left( \frac{\partial \gamma}{\partial \sigma}(t, \sigma), \, \frac{\partial \gamma}{\partial t}(t, \sigma) \right) \frac{\partial \gamma}{\partial t}(t, \sigma)
\end{align} Now, set $\sigma = 0$ in which case
$$\frac{\partial \gamma}{\partial t}(t, 0) = \frac{d\gamma}{dt}(t) \,\,\, \text{ and } \,\,\, \frac{\partial \gamma}{\partial \sigma}(t, 0) = \xi(t)$$ Consequently, the equation above turns into
\begin{align}
0 =& \nabla_{\frac{d \gamma}{d t}(t)}\left( \nabla_{\frac{d \gamma}{d t}(t)}\, \xi(t)\right) + R\left( \xi(t), \,\frac{d \gamma}{d t}(t) \right) \frac{d \gamma}{d t}(t)
\end{align}
Recall that $$\nabla_{\frac{d \gamma}{d t}(t)} \nabla_{\frac{d \gamma}{d t}(t)} = \frac{D^2}{dt^2}$$ as a notation and we arrive at the Jacobi equation
$$\, \frac{D^2 \xi}{dt^2} + R\left( \xi, \,\frac{d \gamma}{d t}(t) \right) \frac{d \gamma}{d t}(t) = 0$$
I assume your last question about the sphere with changing radius is asked out of confusion. The topic of Jacobi equations and Jacobi fields does not require for the metric and the whole geometry to be changing. The geometry usually stays fixed. If the geometry changes with respect to some parameters, simply all the quantities involved in the Jacobi equation will additionally depend on these parameters.