I guess I don't follow your analysis.
People doing mapping tasks will use an editor and not really see the change.
People consuming the data will also mostly use tools, tools that likely run much faster.
I've written some code to chop up overlapping gis areas into ways and relations (to match the current data model of references to shared nodes). The input to that code is pretty close to the proposed data model, so not going to be more difficult to do that processing (as an example of a task that doesn't just use 3rd party tools).