I would go for the first one, the complete EV routes as it easier to handle. I think that stages may be transnational sometimes, i.e. knooppuntnet, part Germany 3 (it’s the same part as knooppuntnet connection between Switzerland and France, a bit less than 1 km
I have added a column to knooppuntnet at the wiki - a better column name would be very welcome.
That would be (in my opinion) a much better segmentation of the routes than current one. There would be new GPX tracks availaible I think, if I look in knooppuntnet at the segmentation of EV 4
If we reach a consensus we would update the wiki accordingly. Maybe adding a section in the wiki discussion page too.