Thank you for reporting a bug to Unity.
After reviewing the behavior, we've confirmed it aligns with the current design and intended use of the feature. We understand this may differ from your expectations or workflow.
The hierarchy of objects has no effect on how the patches of different area types are computed in the NavMesh. Only the indexes of the overlapping area types matter for choosing the resulting area type. The higher index takes precedence, as explained in the "Navigation Areas and Costs" page in the documentation https://docs.unity3d.com/Packages/com.unity.ai.navigation@2.0/manual/AreasAndCosts.html#area-types .
> If several objects of different area types are overlapping, the resulting NavMesh area type will generally be the one with the highest index. There is one exception however: Not Walkable always takes precedence, which can be helpful if you need to block out an area.
We will close this case as 'As Designed.' If you have feedback on how the feature could better meet your needs, please let us know - we value your input and consider it in future improvements.