Generally one of three reasons, I think.

1- Either because that's the source the submitting person first saw and didn't think of chasing down the root source before submitting;

2- or because the non-root source has added context and/or better writing explaining the situation;

3- or because (least common imo) submitter has a vested interest in promoting the specific site they link to.

Dang / other mods (are there others? I can't remember) are generally good at updating submission links to either the root or to a better write-up, when it doesn't seem that the one submitted does have a good claim to be the best site chosen for a story. (Of course they're more likely to do it if people helpfully provide the suggestion to flag that it could be improved, and suggesting a better link - as you did.)

But perhaps it would be worth having a small note on the submission form asking people to briefly reflect on whether the link they are submitting is indeed the best form of the story, or whether they could spend another minute following a couple of links (or doing a quick search) to find a possible better one?