It is true, that in nature there is only one true independent variable, time. All others are "pseudo-independent". They are variables humans bless as independent in order to answer what-if scenarios and to establish mathematical models of systems byways of separation of variables. The common term for these "pseudo-independent" quantities is generalized coordinates.
Looking at a complex mechanical system, like a human launching a ball while riding on a skateboard. First, we decide what the degrees of freedom are and assign generalized coordinates to them. These are simple measurable quantities of distance, angle or something else geometrical forming a generalized coordinate vector $$\boldsymbol{q} = \pmatrix{x_1 \\ \theta_2 \\ \vdots \\ q_j \\ \vdots} \tag{1}$$ In this example there are $n$ degrees of freedom. All the positions of important points on our mechanisms can be found from these $n$ quantities. If there are $k$ kinematic hardpoints (such as joints, geometric centers, etc) then the $i=1 \ldots k$ cartesian position vector is some function of the generalized coordinates and time
$$ \boldsymbol{r}_i = \boldsymbol{\mathrm{pos}}_i(t,\, \boldsymbol{q}) \tag{2}$$
Here comes the chain rule part. With the assumption that (2) is differentiable with respect to the generalized coordinates, and that contact conditions do not change due to separation, or loss of traction, the velocity vectors of each of the hardpoints is found by the chain rule
$$ \boldsymbol{v}_i = \boldsymbol{\mathrm{vel}}_i(t,\,\boldsymbol{q},\,\boldsymbol{\dot{q}}) = \frac{\partial \boldsymbol{r}_i}{\partial t} + \frac{\partial \boldsymbol{r}_i }{\partial x_1} \dot{x}_1 + \frac{\partial \boldsymbol{r}_i }{\partial \theta_2} \dot{\theta}_2 + \ldots + \frac{\partial \boldsymbol{r}_i }{\partial q_j} \dot{q}_j + \ldots \tag{3} $$ where $q_j$ is the j-th element of $\boldsymbol{q}$, and $\dot{q}_j$ its speed (being linear or angular).
The above is not a division of infinitesimals, but the multiplication of a partial derivative $\tfrac{\partial \boldsymbol{r}_i }{\partial q_j}$ with the particular coordinate degree of freedom speed $\dot{q}_j$.
Maybe you are more comfortable with this more rigorous notation using partial derivatives that what you have seen so far. The term partial derivative means, take the derivative by varying only one quantity and holding all others constant. This is what allows us to use pseudo-independent quantities $q_j$ for the evaluation of the true derivative with time (the one actual independent quantity).
The same logic is applied to higher derivatives as well
$$ \boldsymbol{a}_i = \boldsymbol{\rm acc}_i(t,\boldsymbol{q},\boldsymbol{\dot q}) = \frac{\partial \boldsymbol{v}_i}{\partial t} + \ldots + \frac{ \partial \boldsymbol{v}_i}{\partial q_j}\, \dot{q}_j + \ldots + \frac{ \partial \boldsymbol{v}_i}{\partial \dot{q}_j} \,\ddot{q}_j \tag{4} $$
The last part might be a bit confusing, but when you express it in terms of actual degrees of freedom it might be clear. Consider the degree of freedom $\theta_2$ and its time derivatives $\omega_2$ and $\alpha_2$. Then the terms $\frac{ \partial \boldsymbol{v}_i}{\partial \theta_2} \omega_2 $ and $\frac{ \partial \boldsymbol{v}_i}{\partial \omega_2} \alpha_2 $ are more clear I hope, as $\boldsymbol{v}_i$ depends on both the position $\theta_2$ and the speed $\omega_2$.