Steps to reproduce:

1. Open attached project
2. Notice that 'Auto Rotation' is enabled in player settings and that 'Landscape Left' and 'Landscape Right' are the allowed orientations
3. Build the project
4. Open project in Xcode
5. Change the allowed orientations to 'Portrait' and 'Upside Down' in Xcode (disable Landscape orientations)
6. Build and run the Xcode project on a device
7. Notice the custom splash screen will be in Portrait (or Upside Down, depending on device position) but Unity splash screen and the application itself will only be in Landscape Left or Landscape Right orientation.

DUT:
iPad Mini 2 (iOS 7.1.2)
iPad 2 (iOS 8.1.2)
iPhone 6+ (iOS 8.0)
Reproduced on all three.

Reproduced with: 5.2.3f1, 5.3.0f1