If an actor contains multiple primitive components, it uses all of them for calculating navigation bounds even if some of the primitives are not marked as navigation relevant. Toggling navigation relevancy of the primitives once in the scene also does not alter/correct which primitives interact with navmesh generation.
Customer provided solution:
Expected result: The navmesh is cutout around the original, navigation relevant primitive, and the second primitive component does not cut the navmesh.
Actual Result: Navmesh is cut out around each of the volumes despite one not being listed as navigation relevant.
There's no existing public thread on this issue, so head over to Questions & Answers just mention UE-160479 in the post.