In the probability expression, $X\leq x$ is an event. It represents the set of outcomes whose $X$ measure is less than $x$.
It is quite permissable to condition on an event. $\mathsf P(Y=y\mid X\leq x)$ is a valid expression, and indeed it is true that:
$$\mathsf P(X\leq x, Y=y) = \mathsf P(Y=y\mid X\leq x)~\mathsf P(Y=y)$$
However, you do not want to use that.
$$\begin{align}\mathsf P(X\leq x, Y=y) ~ & = ~ \mathsf P(Y=y)\cdot\mathsf P(X\leq x\mid Y=y) \\[1ex] & = ~ p_Y(y)\cdot \int_{-\infty}^x f_{X\mid Y}(s\mid y)\operatorname d s \\[1ex] & = ~ \int_{-\infty}^x p_Y(y)\,f_{X\mid Y}(s\mid y)\operatorname d s \\[1ex] & = \int_{-\infty}^x f_{X,Y}(s, y)\operatorname d s \\[1ex] & = ~ \int_{-\infty}^x p_{Y\mid X}(y\mid s)\, f_X(s)\operatorname d s \end{align}$$
Although that's not so much a proof of anything, as a definition of how those measures must behave.