Why does the below step result in a chain rule? Intuitively, I would just differentiate it against y and x resulting in $-y^{-2} = -\sin{x}$.
Khan Acad mentioned something about relating y = y(t) and x = x(t), but my brain is struggling to comprehend why it can just be related like this... (Though I could just be getting it completely wrong)

I actually think it is easier if you separate out differentiation from derivatives. Differentiation is the process of converting an equation of variables to an equation of differentials. A derivative is a ratio of derivatives. I think that separating these processes makes the whole of calculus easier to understand.
So, in your case, you have:
$$y^{-1} = \cos(x)$$
If we just differentiate it, we get:
$$ -y^{-2}\,dy = -\sin(x)\, dx$$
Here, no variable has a privileged place. We aren't differentiating with respect to anything. Every expression is followed by the differential of the variables.
The question wants $\frac{dy}{dt}$. To do that, start by solving for $dy$:
$$ dy = \sin(x)\,y^2\,dx $$
Now, just divide both sides by $dt$ (you can do anything you want to an equation, as long as you do it to both sides - even dividing by a brand new differential):
$$\frac{dy}{dt} = \sin(x)\,y^2\,\frac{dx}{dt}$$