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Xela stated to be pedantic, pairings are usually determined by rules, not by personal decision of TD?.
In the AHA, the tournament director makes a series of manual pairings, allows the software to perform the rest of the pairings, and then re-pairs specific players as the tournament director sees fit. I can not say that every TD does this. I can not say that it happens every tournament. I can say that this is done in every US Open (the big tournament at the US Go Congress) that I have attended. And that this is done at every major tournament that I have attended.
The assignment of pairings is not determined by rules, other than the TD will assign pairings.
I know that for the Dutch Championship, there is a very specific procedure that must be followed, which defines how to sort the players within a band and who they should be matched with based on that.
Different tournaments use different methods. E.g., in Norway they use random pairings within the same MM group. For some tournaments, it is specified in the tournament rules, for others it is not and so tyically up to the TDs.