To reproduce:

1. Open the project, attached by the user (New Unity Project 2.zip)
2. Open the "Scene" scene
3. Enter Play mode
4. The console will show the bone's position. Observe how it changes only after FixedUpdate has been called a couple of times

Expected: Animation.Update method updates bones immediately when it is called

Reproduced in 5.5.2p4, 5.6.3f1, 2017.1.0f3, 2017.1.0p4, 2017.2.0b7, 2017.3.0a4

Won't fix: The Animator is not updated before it's visible, because the cullingMode is not set to AlwaysAnimate.
Setting the culllingMode to AlwaysAnimate makes the animator update the bones immediately.