Your link [2] came 1 hour before your link [1]. Don't think there's anything malicious going on there, they just marked the one that came later as a dupe.
If marking something as a dupe would transfer points to the duped thread I would agree. I would also agree if it was marked as a dupe within a reasonable amount of time. But marking a popular, 12 hour old thread as a dupe of a marginally older, unpopular thread and giving it the ranking of the unpopular thread feels wrong and doesn't respect the intent the community has expressed by voting.
This seems a reasonable argument, and I think the mods should adopt your idea of transferring the points to the duped thread (and possibly the comments?)
And the post ranking!
I assume points being transferred would cover the post ranking.
The ranking is based on arrival rate of points, ratio of comments, total points, and other factors including manual moderator boost or demotion.
The news on this broke yesterday evening, and at one point both threads were on the front page. In my opinion the time to mark one as a dupe of the other was then, not 12 hours later. Especially in light of the fact that the 2nd comment on the now-marked-dupe post was a link to the earlier discussion, and in spite of that, discussion gravitated to the submission linking to github over the one linking to facebook's PR response.
Even if it's not malicious, that policy should be reconsidered then, because it can make interesting front page discussions just disappear.