Algorithm that deside if there are two words $x$ and $y$ in the same length such that $x\in L(A_1)$ and $y\in L(A_2)$
Consider the NFA $A_1=(Q,\Sigma,q_0,F_1,\delta_1)$. Observe that an accepting run of $A_1$ induces an accepted word. That is, we don't really care about the alphabet of the automaton if we only want to consider word length.

Thus, instead of constructing the intersection automaton directly, first change the alphabet of both automata to be $\Sigma=\{a\}$, by changing the letters in all the transitions to $a$. That is, for a transition $\delta_1(q,\sigma)=q'$, change the transition to $\delta(q,a)=q'$.

Now construct the product automaton, and check emptiness.

I'm leaving the correctness proof as an exercise.