As a newbie, I'm months late to this party but maybe I can still contribute. Back in the stone age of computer software, I used to develop some of it. As a ICT-dinosaur and amateur genealogist, Mikechristopher's great question resonated with me.
Back in the stone age of ICT we used to develop 'relational databases'. That meant that the 'data records' were separate from the many and various 'interrelationships' that could exist between these data records. Updating data records would't change the interrelationships. Adding or updating interrelationships wouldn't change the data records. Users were 'presented' with the data and interrelationships that were relevant to their queries.
The same principle is true today for almost all genealogy websites/software. We can update the data for a 'person' without changing family relationships. We can also change the relationships without changing the 'person' data. The main limitation of popular websites and offline-software is that the choice of relationships is limited to the obvious family ones: father, mother, spouse, child. Technically it would be a no-brainer to add data and relationships such as 'possible birth-date, possible death-date, possible father, possible mother, possible child, possible marriage, possible residence', etc. I suspect that the decision to limit the options is more driven by marketing (to beginners) than by a lack of technical capabilities.
Mikechristopher's question helped me to look into the difference between 'person-based' record-keeping' and 'evidence-based' record-keeping. Ideally, these are not mutually exclusive. Popular websites/off-line software does however tend toward 'person-based' record keeping.
Like McGroger, I also use family tree offline (synched with Ancestry online). I like his tips and I intend to use these!
I'm a relative newbie but it seems to me that everyone has to figure out how best to keep track of 'people facts', 'source documents' and (possible) 'relationships' separately. I googled 'genealogy separate people relationships sources' and found software I'd never heard of before!
Mike