It is not possible to select + apply multiple individual prefab overrides at the same time.

To reproduce:
1) Create a new prefab
2) While looking at the game's scene (i.e. not prefab mode), modify multiple properties on the prefab
3) In the Overrides dropdown, select multiple changes & click apply

Notice thet only one change is applied

Not a regression- introduced with conception of new prefab workflows

Some work has been done on this. See comment https://fogbugz.unity3d.com/f/cases/1106861/#BugEvent.1071275834