First note if $\epsilon$ = 0, then $\Delta_{\epsilon} \equiv$ 0, and we have something uninteresting:
$$
\ S(f+g,\Delta) = \displaystyle\sum_{k}^{n-1} M_{k}(f+g)(x_{k+1} - x_{k}) = \displaystyle\sum_{k}^{n-1} M_{k}(f+g)(0) \equiv 0
$$
Otherwise if we don't permit equality, we can recover the definition of the upper integral as $\Delta_{\epsilon} \rightarrow 0$. That is
$$
\ (U) \int^{a}_{b} f \ dx = \inf \{U(f,\Delta_{\epsilon}) | \text{where} \Delta_{\epsilon} \text{is any partition of [a,b]}\}
$$
But $\Delta_{\epsilon} \neq 0$, so as Uzman writes, $U(f)\leq S(f,\Delta_\varepsilon ^1) < U(f)+\frac{\varepsilon}{2}$
Moreover, $\epsilon > 0$ by convention. If not, we would have many trivial results.
In regard to the green box, what you write is not exactly correct, the inequality must hold for all $\epsilon > 0$, that's the beauty. Any value you want, there is another value, smaller yet, that the inequality holds for.