Great concept. Above all, I really do hope that they add some form of mark making to the game. This would allow for some great gameplay possibilities, including this "Points of Interest" idea to some extent.
That said, the more I see of map websites the less I agree with them. For the static map they have been useful, but if procedural maps come in then I can't see the need for them. Your suggestion for in game mapping would be helpful for some people sure, but the application interface could easily be ported to an external website and generate a map for all to see, possibly with info about your location and base etc.
Edited:
Because it would be cool to find other maps. Like if u kill someone or break into someones place their maps could contain codes, locations, information, etc.
Im pretty sure no-one's gonna write all that stuff down and leave it in an unlocked box for someone to just find, but it could be used as a way to guide players to a new town or place of interest if it was implemented procedurally. So basically every new location would have a number of maps/directions to find it spawning in the world, giving people who find them an edge over those who are just randomly looking around for stuff. Wooly concept but I think it has some potential.