kartonage
This is not odd behaviour of osm data, this is (mostly) intended styling chosen by the map style maintainers. I suggest to not try to change osm data just so it can be rendered in some way. You can suggest changes to the map style to the maintainers (you are probably referring to the "standard" map style): https://github.com/gravitystorm/openstreetmap-carto

If something is destroyed the destroyed: prefix will be the way rather than trying to cover it with some other element.