I'm reading this text:
I'm a bit lost about why the sentence is in bold. Why is the word 'despite' being used? I can see that the derivative of $\frac{-1}{x} = \frac{1}{x^2}$, but why is this explained with the word 'despite'? What is the point?
Even more so, what is the point of learning about indefinite integrals?

As pompelle mentioned in the comments, the issue is that the set of functions
$$ -\frac1x+C $$
don't contain all the functions whose derivative is $1/x^2$. It is true that the exemplar is simply $-1/x$, and of course a constant can always be added, but because $-1/x$ is in two disconnected pieces (each of which is continuous), different constants can be applied to each piece.
What is being emphasized is that by convention, we don't have to write
$$ \begin{cases} -\frac1x+C_1 & x < 0 \\ -\frac1x+C_2 & x > 0 \end{cases} $$
Instead, for the sake of brevity, we write just
$$ -\frac1x+C $$
with the provision that each separate piece of the function in question can have a separate constant added to it.
ETA: Here are some pictures to depict what I mean. If you just write
$$ -\frac1x+C $$
then strictly speaking, you only get $-1/x$, along with all the functions that are $-1/x$ shifted up or down by a constant amount across the entire $x$-axis, as shown below:
If, on the other hand, you write
$$ \begin{cases} -\frac1x+C_1 & x < 0 \\ -\frac1x+C_2 & x > 0 \end{cases} $$
you get all of the above, plus in addition, you get those functions where the two halves of $-1/x$ are shifted up or down by different amounts, as shown below:
What the book is saying is that they're engaging in a slight abuse of notation whereby the first expression is understood to mean the same thing as the second, larger (and more rigorously correct) expression.