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The answer is no in general. Indeed, suppose $B=\{E,F\}$ and $k(x,A)$ equals $1/2-f(x),f(x),1/2-f(x),f(x)$ if $A$ is $E\setminus F,E\cap F,F\setminus E,Y\setminus E\setminus F$, respectively, where $f\colon X\to[0,1/2]$ is not $\Si_X$-measurable. Then $k(\cdot, U)$ is measurable for each $U\in B$ but not for $U=E\cap F\in \Sigma_Y$.
However, your desired conclusion will hold if $B$ is an algebra. Indeed, suppose that $B$ is an algebra and consider the set $C$ of all $U\in\Si_Y$ such that $k(\cdot, U)$ is measurable. Clearly, $C$ is a monotone class. Hence, your
desired conclusion follows by the monotone class theorem.