Repro steps:
1. Open QA attached project "repro"
2. In the top menu bar select Build -> Prefab
3. In Hierarchy select game object "go0" and observe its Rect Transform coordinates
4. In Project Window select "MyPrefab" and observe its Rect Transform coordinates

Expected: the coordinates of both Rect Transform components match
Actual: only the Z coordinate matches

Reproducible with: 2017.3.0a1, 2017.4.3f1, 2018.1.1f1, 2018.2.0b4, 2018.3.0f2, 2018.3.6f1
Not reproducible with: 2017.1.3p4, 2017.2.3f1, trunk revision 5371f9df378a

Notes: child objects are also created with wrong X and Y coordinates.

Workaround: It is possible to create correct prefab manually.