I'm not sure what documentation you are referencing, but https://wiki.openstreetmap.org/wiki/Tag:highway%3Dstop#Tagging_minor_road_stops is pretty clear on how to map things. Putting stop signs at stop positions is a perfectly valid and more detailed way to map than putting them at way intersections.
Further more, it is the only correct way to tag them where only 1 road has to stop.

This needs to be corrected since data consumers, especially routers are affected by this. 