Reproduction steps:

1. Open "MinimalRepro.zip" project
2. Right click "SetupAnimationController" -> "Mod" -> "Setup" -> "NewAnimationController"
3. Click on the new "animationController"
4. "Window" -> "Animator"

Expected Result: "BUG1" and "BUG2" State Machines are in different (set in code) places
Actual Result: "BUG1" and "BUG2" State Machines are on top of each other

Reproduced with: 2017.3.0a5, 2017.2.0b9, 2017.1.0p5, 5.6.3p2, 5.5.4p4, 5.4.5p5

Note:
The position doesn't change, even thought through Debug.Log you can see that the Vector3 is changed.
Changing the position on the State Machine creation works, but after that ChildAnimatorStateMachine.position doesn't affect the State Machine