Changes in Rect Transform are not applied to prefab variants

Steps to reproduce:

1. Create an empty game object and add Rect transform
2. Drag the empty game object to project tab to make prefab
3. Create prefab variant(right click on the prefab >> create >> prefab variant)
3. Make changes in the Rect Transform of the prefab variant
4. Make sure autosave is checked on or user needs to save it manually
5. Open prefab variant again to check changes has been applied to it or not

Check the attached video to reproduce the issue

Expected Result: Changes should be applied

Actual Result: Changes are not applied

Occurring with:
Version 2018.3.0a2 (e9113db2e9bf)
Branch: prefabs/improved

Version 2018.3.0a3 (8235364df44d) Personal
Branch: prefabs/improved

Environment:
Windows 10 and Mac 10.13

This is by design. Default override properties do not propagate to Prefab instances, including the instance of a base Prefab inside a Prefab Variant. See the documentation section "Alignment is specific to Prefab instance":
https://docs.google.com/document/d/1MjxUjT1krD4iB91kKpUIAF7NMr3gUrvo5x3EXi9AGbw/edit#heading=h.hq5our40rul5