The problem is caused by the fact that the height of the bounding volume of all the source geometry changes when we add new objects in the scene, like when adding and stacking new cubes on top of each other or when an object falls indefinitely. The change in height is mistakenly detected by all the NavMesh tiles and not only the modified tiles, thus the build process triggers an update in all the tiles.

Proposed user-side workaround usable immediately:
When preparing the list of source geometry for the NavMeshBuilder.UpdateNavMeshData() function, go and include two dummy NavMeshBuilderSources placed high enough and low enough so that they will forever be above/below any of the other source meshes. Don't exaggerate with the height because this will affect the precision of the build process. Keep the difference in height between them somewhat less than 32000 x navMeshBuildSettings.voxelSize .
They will force the bounding volume of the build process to be stable (the same) during every UpdateNavMeshData. This in turn will stabilize the internal hashes of the NavMesh tiles. If necessary keep these two sources small enough for them to not generate any NavMesh patches.