Andrew, I would actually consider that a slightly different use case. We do plan on supporting partial updates like you describe, in the same way that Cesium ion currently supports uploading your own local terrain and combining it with Cesium World Terrain, you would do the same thing with 3D Tiles. The feature request for this is open here (which I've just bumped with your post):
For removing specific buildings, I imagine that would be useful when you either want to put something that isn't 3D Tiles there (such as a glTF model of a new proposed building) or perhaps just because you want to see the underlying terrain underneath a specific property perhaps.