I was under the impression that: there should always be a node on the intersection when ways are physically attached to each other. If ways cross each other without physical contact (e.g. bridge, tunnel) there shouldn’t be a node on the intersection.

Any non-physical attributes like turn restrictions, permissive access, way types (tram, road), etc. should be added as properties (relations?) to the ways and nodes. Permissive access and turn restrictions should not play a role with regard to placing nodes on road intersections.

So, IMHO, in this example the nodes on the intersection in image 4 are placed more or less correct. One could dispute if 6 nodes are needed (upper road is split into two just before the junction) or maybe even 3 (if the lower road is combined into one just before the intersection) as alternatives…But the current solution seems correct to me.