The track layout varied over time. The first photo from 1883 shows a much more limited layout and the major expansion seems to come in the late 80's early 90's. I think once the layout was essentially finished the track layout was not significantly changed but could not prove it.
Now why there were put in a particular position at a particular time is difficult to say. As it is unlikely there ever will be a definitive answer just some thoughts:
The Roundhouse was actually planned to be Brick but was constructed in Stone, but the location would not allow it to be extended without considerable fill into Park Gulch. Seems an odd choice.
I can not be certain but think Track 9 predated the Roundhouse in its general direction. Was it part of an original wye?
When the Roundhouse was extended with wooden sections presumably Track 9 was then used for the Rotary, it was later when the wooden extension was replaced with a limited 3 bay extension.
Did the change in the extensions have an impact, the later seems to have been bigger.
Did relaying the track have an impact
Was there another factor not known
It has been a very long time since the rail was removed, you come across certain traces, rotted ties that were buried, locationally the inspection pits are probably the best reference.
I know the 1918 map is not precise, probably shows everything relative to each other but then it was mainly done as an inventory.
Photographs, well there is not a complete set showing every aspect at a given time, I think most of the photos are not dated.
Some photos are much clearer than others. Some angles are missing.
I have certainly assumed something from one photo and then another has appeared which has changed my view.