so... I am doing the reputation science that led to that bugreport, as well as the updates on the wiki here:
http://www.bay12forums.com/smf/index.php?topic=175195.0Relationships and reputation is indeed very interconnected. As far as I can tell, most reputation has a relationship status associated with it, so friends have a friend reputation, grudges a grudge reputation. Familial relationships are a separate thing here, so is romance. I am still not sure how everything is exactly stored, it seems at the least a part of the relationship is stored on a per-unit level, another part on a hist-fig level and yet another part on an entity level. (DFHack lua reading results in entities carrying the big reputations, such as bard, poet, killer, defender of the weak, and histfigs carying the interpersonal ones, so quarelling, good for bussiness, friends, friendly, source of info. But there's also, when you do a dance, that adventure mode npcs know you as a dancer now, but it hasn't propagated to the entity yet, nor is it stored at the histfig level, so I suspect there's another place this stuff is stored which isn't the relationship ids in the unit)
But yeah, this also kind of blew my mind when I saw it, as it seems from the dfhack values and string dump that all of the reputations have an associated relationship status (considers quareller, considers poet). But you don't see them in fort mode for some reason???
I still think the main problem here is dwarves' chatting radius being super small, but the lack of reputation-related relationships showing up indicates there's other messiness going on as well.