I've always maintained my own sources as original + diff rather than modified + diff, and reading this discussion made me think about why.
The appealing thing to me is that it's symmetric: when you get a new version you have old, new, and diff, and the diff relates to new in the same way as it does to old. I think most people would find original + diff less surprising. Of course the existence of patch -R makes this all a minor point. (Apologies if this is way out of date, I'm reading this through a very flaky newsfeed that just delivered a batch of articles from a week ago.)
