I read a proof which used the following type of argument:
Assume we draw two random variables $x_1, x_2$ indepenently. Let $y$ be another random variable, that directly depends on $x_1$ and $x_2$ (e.g. $y$ is the sum of both). Suppose that under the assumption, that we have drawn $x_2$ already, the bound $\mathbb{P}(y \leq \varepsilon) \leq \frac{\alpha}{x_2}$ is true. Let $f$ be the pdf for $x_2$. We then get $$ \mathbb{P}(y \leq \varepsilon)\leq \int_0 ^\infty \frac{\alpha}{x_2} f(x_2) \ dx_2 .$$
Intuitively this makes so much sense, but I dont know why exactly this is true. What is the underlying probability theoretic principle that allows us to conclude the second bound?
Let me first clean up the notation in your proof. I am used to writing random variables as capital bold letters so they're easily distinguishable from non-random quantities. I don't insist on that convention, but it is important to distinguish a random variable from a possible value it can have. In particular, it makes no sense to integrate with respect to a random variable!
Here, we can use the law of total probability for continuous random variables: $$ \mathbb P(A) = \int_{-\infty}^\infty \mathbb P(A \mid \mathbf X = x) f_{\mathbf X}(x) \,dx. $$ In this problem $A$ will be the event $\mathbf Y \le \varepsilon$ and $\mathbf X$ will be $\mathbf X_2$. We should assume that $\mathbf X_2$ can never take on negative values, or else the bound in the question can't possibly hold; therefore it is okay to integrate from $0$ to $\infty$ instead. This gives us $$ \mathbb P(\mathbf Y \le \varepsilon) = \int_0^\infty \mathbb{P}(\mathbf Y \leq \varepsilon \mid \mathbf X_2 = x_2) f(x_2) \,dx_2. $$ Using the inequality $\mathbb{P}(\mathbf Y \leq \varepsilon \mid \mathbf X_2 = x_2) \leq \frac{\alpha}{x_2}$, we get the final bound you wanted.