I can't tell you why they went to a 2 & 1 engine set up, but it was the standard way of doing things for years when traffic was heavy. Jimmy B's dispatcher's sheets show lots of 3 engine trains like this.
With the 2X1 set up, the head end is going to pull 2/3 of the train, so 2/3 of the way back, the slack will change from stretched to bunched and stay that way all the way up the hill. Putting all 3 up front would put too much strain on the head end and likely pull a drawbar on wooden cars. We used to run some tripleheaded passenger trains out of Chama, but we had heavy steel underframed cars that were built as SG cars and able to take more abuse than any ng equipment could enflict on it.
Putting the helper int he middle (1x1x1) would take extra switching and be unnecesary as the wood cars can put up with 2 engines pulling on them. There might be additional issues with slack action with the 3rd engine in the middle if all 3 engines were not pulling equally.
On 2 engine train they would cut the helper in mid-train if the train consisted of lots of empty wood cars on the rear. Shoving on the empty pipe gons and flats tended to buckle them. I've seen video of a helper shoving a train up the hill and a flat car a few ahead of the caboose is bowed up nearly a foot in the center. I suppose they might have done the 2x1 set up with the rear engine midtrain, but I've never seen a pic of that.
If 4 engines were used, they used a 1x2x1 set up. There are lots of pics of stock trains on Marshall with that set up. The reasoning here was if they stalled, the front 1/2 could be taken to the top using 3 engines, the middle 2 could drop back to the rear 1/2 and using the remaining 3 engines, get the second 1/2 up the hill.