How to reproduce:
1. Download attached project files and open "test" Scene
2. Enter Play mode. Notice now the world-space location in Awake is printing the prefab location as opposed to the location passed to instantiate:
Parent(Clone): World-space location: (-10.0, 20.0, 0.0)
Child: World-space location: (-10.0, 20.0, 0.0)

Not reproduced:
1. Open project with Unity 5.6.3p2 and hit "play". Notice that "World-space location" printed in SpawnLog.Awake now outputs location as expected according to SpawnPrefab-script:
Parent(Clone): World-space location: (50.0, 100.0, 0.0)
Child: World-space location: (50.0, 100.0, 0.0)

Actual result: Instantiate(Prefab, new Vector3(50, 100, 0), Quaternion.identity) applies world position incorect in Debug.Log(transform.postion) after Awake() function call

Reproduced with: 5.6.3p4, 2017.1.1p3, 2017.2.0f1, 2017.3.0b2
Not reproduced with: 5.6.3p2, 2017.1f1, 2017.2.0b8, 2017.3.0a5
Regression since: 5.6.3p3
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Fixed in 2017.1.2p3, 2017.2.0p1, 2017.3.0b5