[guided]The point of the strengthened EVI hypothesis is that the exceptional set of times does not depend on the comparison measure. Let $A_\rho:=A_\rho((a,b+\varepsilon))$ and $A_\eta:=A_\eta((a,b+\varepsilon))$. These are Borel subsets of $(a,b+\varepsilon)$ with full $\mathcal L^1$-measure. Since $\rho_u,\eta_v\in\operatorname{Dom}(\mathcal E)$ for every positive time, the measures $\eta_{t+q}$ and $\rho_{t+r}$ are valid comparison measures whenever $t+r,t+q\in(a,b+\varepsilon)$.
We now justify the phrase "for almost every triple." The set of triples $(t,r,q)\in[a,b]\times(0,\varepsilon)^2$ for which $t+r\notin A_\rho$ has zero $\mathcal L^3$-measure by Fubini's theorem, because for each fixed $(r,q)$ the bad set of $t$ is a translate of a null subset of $(a,b+\varepsilon)$. The same argument gives zero $\mathcal L^3$-measure for the triples with $t+q\notin A_\eta$. Hence, outside a null set of triples, both EVI inequalities may be applied simultaneously.
For such a triple, applying the EVI for $\rho$ at the time $t+r$ with fixed comparison point $\eta_{t+q}$ gives
\begin{align*}
\partial_1 D(t+r,t+q)+\lambda D(t+r,t+q)\le 2\mathcal E[\eta_{t+q}]-2\mathcal E[\rho_{t+r}].
\end{align*}
Applying the EVI for $\eta$ at the time $t+q$ with fixed comparison point $\rho_{t+r}$ gives
\begin{align*}
\partial_2 D(t+r,t+q)+\lambda D(t+r,t+q)\le 2\mathcal E[\rho_{t+r}]-2\mathcal E[\eta_{t+q}].
\end{align*}
The two right-hand sides are finite because both comparison measures lie in $\operatorname{Dom}(\mathcal E)$. Adding the two displayed inequalities cancels the energy terms and gives
\begin{align*}
\partial_1D(t+r,t+q)+\partial_2D(t+r,t+q)+2\lambda D(t+r,t+q)\le 0.
\end{align*}
Because $D$ is locally absolutely continuous in each variable, the partial derivatives appearing here are locally integrable on the compact averaged region. Therefore Fubini's theorem permits integration of the inequality over $(r,q)\in(0,\varepsilon)^2$, and the standard differentiation rule for Steklov averages of absolutely continuous functions gives
\begin{align*}
F_\varepsilon'(t)=\frac{1}{\varepsilon^2}\int_0^\varepsilon\int_0^\varepsilon \bigl(\partial_1D(t+r,t+q)+\partial_2D(t+r,t+q)\bigr)\,d\mathcal L^1(r)\,d\mathcal L^1(q)
\end{align*}
for $\mathcal L^1$-a.e. $t\in[a,b]$. Averaging the preceding pointwise inequality over $(r,q)$ gives
\begin{align*}
F_\varepsilon'(t)+2\lambda F_\varepsilon(t)\le 0.
\end{align*}[/guided]