why is $\Pi_2$ smaller than $NP\cap coNP$
You seem to be using the following definition of $\mathsf{NP} \cap \mathsf{coNP}$: it consists of all languages of the form $L_1 \cap L_2$, where $L_1 \in \mathsf{NP}$ and $L_2 \in \mathsf{coNP}$. However, in reality $\mathsf{NP} \cap \mathsf{coNP}$ consists of all languages $L$ such that $L \in \mathsf{NP}$ and $L \in \mathsf{coNP}$.