One thing with your current POI - IMO it would be best to be able to save one's own POI in gpx (waypoint) format, so that they are transferable easily to other systems. In essence, this view embraces the "tensions" between requirements of road navigation vs free hiking nav.
Also, modrana should really save the routing if it's closed without the routing being cleared. It happened as I was driving that it must've segfaulted or something, but closed. Then upon reopen, the navigation should be there right away, as is standard in nav software, rather than having to again select where to navigate etc.
Question on this: When the program is updated, does the user_conf reset or remain?
If user changes happen, the app manager will make a backup and then replace it with the package contents by default. apt-get will prompt and ask what to do.
I don't know, but it should be only read, not written, by the program, i.e. remain, not reset.