Thank you for reporting a bug to Unity.
We have reviewed the issue carefully, and in this case, the team is unable to prioritize fixing this bug. There are a number of reasons we make this decision, including the impact and severity of the issue across our user and customer base, and the possibility that future plans may solve the problem in a different way, or that a workaround for the bug may be available.
Today we will be closing this case. Thank you again for taking the time to report this issue, and please let us know if there is anything else that changes the impact or severity of this issue.
Work around note: one way to work around the issue is to place a small cube anywhere lower than the meshes present in the scene. This causes the NavMesh builder to extend its bounds further down and correctly include all meshes in the calculations.