Having trained dealers for many years, I would never allow dealers to stack or separate chips unless the game being played is a Hi-Lo Split game. In that case, I would encourage stacking chips. The dealer procedure should be carried out in a specific fashion that would not slow down the game.
I remember an occasion while training student dealers for an Omaha Hi-Lo Split game. The dealer decided not to stack the cheques because the flop contained three picture cards. Obviously, there was no possibility for a low hand. I told the dealer to stack the cheques anyway. The debate as to why began? The dealer said: "why would I waste my time stacking and separating chips when no low is possible? I said: "during our training, I want all students to get in the habit of separating and stacking cheques whenever dealing a Hi-Lo Split game"...the other reason is, I felt it was not up to the dealer to let the players know that there was no chance for a low hand. The reasons are obvious.
The dealer reluctantly proceeded to burn and turn, the turn and river. In the end, two players had high straights and the pot was split anyway!
To get back to the original question: No...dealers should not stack cheques or chips in any pot unless it is a Hi-Lo Split game.