I think the notation $\delta f(x)$ while possibly intuitive is extremely ambiguous and not well defined. The formula at the end of your post: (with minor notational change)
\begin{equation}
\delta F_{\phi}(\rho) := \dfrac{d}{d \varepsilon} \bigg|_{\varepsilon = 0} F(\rho + \varepsilon \phi)
\end{equation}
is well defined, and unambiguous (as long as you specify the domain and target space of the function $F$). The way to "read" the symbol $\delta F_{\phi}(\rho)$ is "the directional derivative of the function $F$ at the point $\rho$, along the direction $\phi$". If you look at any advanced calculus textbook such as Loomis and Sternberg's Advanced Calculus, you'll see that this is precisely how directional derivatives are defined (some books require $\phi$ to be a unit vector... but that's not needed). In the subject of Calculus of variations, this is often called "the first variation of $F$ at $\rho$, along $\phi$" (or simply, the first variation of $F$). Regardless of what you want to call it, the formula above is well defined, and thus we can apply it to your question.
If we define $f(x) = \displaystyle\int_a^b q(t,x) \, dt$, then we can compute the first variation of $f$ at the point $x$, along $\phi$ as follows:
\begin{align}
\delta f_{\phi}(x) &:= \dfrac{d}{d \varepsilon} \bigg|_{\varepsilon = 0} f(x + \varepsilon \phi) \\
&:= \dfrac{d}{d \varepsilon} \bigg|_{\varepsilon = 0} \int_a^b q(t,x + \varepsilon \phi) \, dt \\
&= \int_a^b \dfrac{\partial}{\partial \varepsilon} \bigg|_{\varepsilon = 0} q(t,x + \varepsilon \phi) \, dt
\end{align}
($:=$ means "by definition")
In the last equality I made use of the Leibniz Integral rule for differentiating under the integral. The quantity inside the integral can be expressed using the multi-variable chain rule as $\dfrac{ \partial q}{ \partial x} (t,x) \cdot \phi$. But if you want to express it as a variation, using $\delta$, then to be proper, you would have to do the following: for each $t \in [a,b]$, define $Q_t(x) = q(t,x)$. Then, the quantity inside the integral is precisely $\delta (Q_t)_{\phi}(x)$ (the first variation of the function $Q_t$ at $x$, along $\phi$). So, what we have shown is
\begin{equation}
\delta f_{\phi}(x) = \int_a^b \delta(Q_t)_{\phi}(x) \, dt.
\end{equation}
And now, if you abuse notation by suppressing the direction of variation $\phi$, and if you're too lazy to define a new function $Q_t$, so that domains etc match up, then you get the claimed formula:
\begin{equation}
\delta f(x) = \int_a^b \delta q(t,x) \, dt.
\end{equation}