Larger sized phones such as the iPhone 6 Plus will not work with the Fallout 4 Pip-Boy replica which comes with the Fallout 4 Pip-Boy Edition.
Bethesda clarified the sizing on their blog stating that the Pip-Boy included will have foam inserts that fit iPhone 6, iPhone 5/5s, iPhone 4/4S, Samsung Galaxy 5 (this is likely to be the Galaxy S5 due to dimension differences), and Samsung Galaxy 4. In addition, using the customizable foam insert you should be able to fit most other popular smartphone devices.
For those using larger sized phones, the Pip-Boy companion app will still be available to use when the game comes out.
Bethesda found more stock of the Fallout 4 Pip-Boy Edition and distributed it around North America but all locations have currently sold out. In the UK, GAME has exclusive rights to the Pip-Boy Edition but is also currently sold out.
Fallout 4 will be available on PC, PlayStation 4 and Xbox One on the 10th November.