How to reproduce:
1. Open the attached Test.zip project
2. In the Project window select Button Variant
3. In the Inspector window open Prefab in the Prefab mode
4. Make some Rect Transform parameters changes
5. Close Prefab and open it again, see that the changes were not applied

Expected: UI Prefab Variants Rect Transform changes are applied
Actual: UI Prefab Variants Rect Transform changes aren't saved

Reproduced on: 2018.2.0x-ImprovedPrefabs, 2018.3.0b5, 2019.1.0a3
Not Reproducible in 2019.1.0a11

Note: Couldn't test on earlier versions because the feature was introduced in 2018.3