Recently I have observed judges stating that the opponent in a one on one game is not allowed to pile shuffle the deck presented to them (in order to change the order, and count to ensure a legal number of cards are present in the deck) supported by MTR 3.9:

Pile shuffling may not be performed other than once at the beginning of a game to count the cards in the deck

Does this prevent opponents from doing so, or do we still allow them to, for example, 3 pile shuffle to reverse a double nickel, or pile shuffle to reorder and count at the same time?

Yes, each player is allowed one pile “shuffle” (count, actually) per game.

Perhaps we can find wording to make that clear; I'll pass that along.

d:^D

Heh - and my wording isn't even as clear as it could be!

One pile, per player, per deck, per game.

Each player can pile their own deck, then pile the opponent's deck, once per game. Note that mulligans do not reset this; we don't want players piling for every mulligan.

d:^D