Applying/Reverting/Placing a prefab makes transform position and rotation dirty even if the position and direction of game object was not changed. Clicking transform -> revert to prefab, cleans a dirty prefab. Reverting a whole prefab does not clean it.

Reproduction steps:
1. Open the attached project
2. Open the scene
3. Select "Prefab Dirty" in hierarchy
4. See that its position and rotation are marked dirty (written in bold)
5. Select "Prefab Clean" in hierarchy
6. Its position and rotation are not marked dirty, although it's made from the same prefab and these values don't differ

Fixed in: 2018.3.0a6

Reproduced on: 5.4.5p2, 5.5.4f1, 5.6.2p1, 2017.1.0b7, 2017.2.0b2