Reproduction steps:
1. Open the attached project ( 5.5b8_test.zip);
2. Open the "m.unity" scene;
3. Enter a play mode;
4. Observe the results in the console.
5. Then quit a play mode;
6. Drag the CubeChild from his parent object;
7. Repeat 3 and 4 steps.

Expected results: RaycastHit.transform and RaycastHit.collider.transform give the same results regardless the object is a parent or child of another object;
Actual results: RaycastHit.transform points on the parent object, but not on the child.

Reproduced on: 5.5.0a3, 5.5.0f2, 5.6.0a5.
Note: not reproduced on 5.4 and 5.3 due to the program crash (Unity crashes when I am trying to open the scene).

The case was closed by design: https://docs.unity3d.com/ScriptReference/RaycastHit-transform.html

"The Transform of the rigidbody or collider that was hit." - that means that if there was a rigidbody associated with the collider hit, it's transform would be returned instead. Note that if you want the other behavior, you might simply use collider.gameObject.transform instead.