These judgeApps threads mention scooping:
http://apps.magicjudges.org/forum/topic/6236/
http://apps.magicjudges.org/forum/topic/13960/

The first one, even if it's somewhat confusing, says that for many years, if a player scooped, then it was assumed he was conceding. Several judges told me this as well, with the explanation that the purpose of this ruling is to discourage mind tricks where a player would make a scooping motion, the opponent would interpret it as a concession, shuffle everything in his deck and then the first player would claim “I was just untapping my lands, now you have nothing on the table.”

Yet, I was not able to find support for this in the MTR.

So the question is: does this still hold? if yes, is the reason I outlined the true one? if not, how is this nuanced?

“Scooping,” before winning the game and communicating such with your opponent, is still considered conceding. While the argument against mind tricks can be a concern, it also falls into a much simpler argument. You have chosen to leave the game early by scooping and, if there's no agreement on if a player won before you scooped, the winner must be the last person sitting in the game. You absolutely must stay in the game until it is clear (and by clear, I mean there was complete evidence that a player had already won, or that you and your opponent have both come to and agreed upon this conclusion) that some player had won that game, and that the game is already over. Until that point, scooping is conceding.

Beyond this explanation, the discussion and answers from those two threads you linked are both rationale toward why this is the case in further detail. Hope this helps!

I should also iterate, that this answer presumes that we have moved beyond a point where we can “repair” this issue. If the player did not mean to concede, and we can fix this, then do so if possible.

Petr, I think my posts in the thread from your second link actually answer your question (and then some); what part(s) can I clarify?

In the first thread, you referred to this as “precedent” rather than “something that's obvious from reading the philosophy or the policy” so I mostly wanted to be sure that it's still in effect.

The particulars I am interested in are:
- Player A genuinely believes he won the match but player B did not acknowledges this. Player A collects his cards and player B says “hey, I may have wanted to do something about it; I don't know if I could, I would need to see the game state again which is not possible now”. Does player A lose?
- Player C is about to be defeated and at the start of his turn, he scoops his lands into one pile. His opponent, player D, believes player C is conceding and collects all of his cards, but then player C just replaces his lands back on the table, claiming that he was just untapping the lands. This is the first time in this match that player C made such a scooping movement but your investigation does not prove that he purposefully did this as a mind trick. Did player C concede?