One reason to discuss the anti-derivative of $\frac{1}{x}$ also for negative $x$ is that some (or many, depending on your audience) students will needs it later on when they learn about ordinary differential equations.
For instance, consider the very simple initial value problem
$$
\begin{cases}
\dot x(t) = x(t), \\
x(0) = x_0.
\end{cases}
$$
As we all know its solution is given by $x(t) = x_0 e^t$ for all $t \in \mathbb{R}$. But assume that you don't know the solution, yet (for instance, if you're a student taking an ODE course) and try to find it by using separation of variables. This gives
$$
\int 1 \, \mathrm{d}t = \int \frac{1}{x} \, \mathrm{d}x.
$$
Assume now that you only learnt that the anti-derivative of $\frac{1}{x}$ is $\ln x + c$ for positive $x$ - it happens to easily that you forget about the sign restriction and just blindly apply the formula. You thus get
$$
t = \ln x(t) + c \qquad (*)
$$
for a constant $c \in \mathbb{R}$ and hence, $x(t) = e^{-c} e^t$. The initial condition finally yields $e^{-c} = x_0$. But this cannot be true if $x_0$ is negative. (Unless one allows for complex $c$ - which is a pain here, since you then need to draw the complex logarithm of a negative number, which means that you cannot use the principal branch of the complex logarithm - in any case, this moves quite deep into the territory of complex analysis for such an innocent differential equation over the real field).
By the way, to add further to the confusion, the same problem does at first glance not arise if you do the separation of variables by using definite integrals instead of indefinite integrals. This gives you
$$
\int_0^t 1 \, \mathrm{d}s = \int_{x_0}^{x(t)} \frac{1}{x} \, \mathrm{d}x,
$$
thus (if makes again the mistake to believe that $\ln x$ were an anti-derivative of $\frac{1}{x}$ for postive and negative $x$)
$$
t = \ln x(t) - \ln x_0 = \ln \frac{x(t)}{x_0}, \qquad (**)
$$
and hence $x(t) = x_0 e^t$ - which is the correct solution formula. Yet, we made the same error as above, by taking $\ln x$ as a (presumed) anti-derivative of $\frac{1}{x}$ even for negative $x$. But the error cancels out for the following reason: Solutions cannot cross equilibrium points, so $x(t)$ always has the same sign as $x(0)$. So if $x(0)$ is negative, so is $x(t)$ and hence the correct computation in $(**)$ for negative $x(0)$ is actually
$$
t = \ln (-x(t)) - \ln (-x_0) = \ln \frac{-x(t)}{-x_0} = \ln \frac{x(t)}{x_0},
$$
which just happens to give the same result as our incorrect (for $x(0) < 0$) computation above.
To sum up: If one learns the anti-derivative of $\frac{1}{x}$ only for positive $x$ and happens to forget about this restriction later on (which is a very easily made mistake), one gets a mess when working with initial value problems. The same method (separation of variables) can then lead either to correct or incorrect result, depending on how precisely one applies the method.
By the way, in case that you find the example discussed above too artificial (because the initial value problem is so simple) - a similar issue appears, for instance, for the logistic equation.