I certainly agree it wouldn't have grown as big as it is with a less pragmatic approach. Entirely.

But there must be a moment when some simplicity or pragmatism must be exchanged for scalability.

Layering is one option. While indeed railroads and roads probably want to be on the same layer, opening hours or pavement need not be. I'm not saying a node may only ever be on one layer. They can easily be duplicated over layers. Just like at boundaries of geographical chunks, (i.e. over the borders of luxembourg.osm.pbf) there are (tens) of thousands of nodes that also appear in Germany, Belgium, the Netherlands once even.