I believe the following is well known after talking to some experts, but I am unable to find a reference for the case with boundary.
Fix a field $F$ and an oriented $n$-manifold $(M,\partial M)$. We have a pairing $H_*(M) \otimes H_{n-*}(M,\partial M) \rightarrow F$ given by taking transverse representatives of the cycles and counting the oriented intersections.
Claim: This pairing is the same as the Poincaré–Lefschetz duality pairing.
Is there a standard reference for this? Or at least an argument that is only a few lines, possibly relying on the closed version of the statement?