Reproduction steps:
1. Open the attached project.
2. Go to Edit > Build Settings > Player settings.
3. Notice, that the Bundle identifier is set to "com.*.AppIdStandalone"
4. Switch to iOS plaform.
5. Notice, that the Bundle identifier is set to "com.*.AppIdIOS"
6. Switch to Standalone platform.
7. Exit the Editor.
8. Navigate to the project folder through the Terminal.
9. Launch the Editor through the Terminal using these launch options: "-quit -batchmode -buildTarget ios -executeMethod BuildScript.Build -logfile ./out.txt".
10. Open the out.txt file in the project folder.
- Debug.Log (EditorUserBuildSettings.activeBuildTarget); and Debug.Log (PlayerSettings.applicationIdentifier); prints the values to the out.txt log.

Actual result:
- Active build target was successfully set to iOS, but PlayerSettings.applicationIdentifier still returns the standalone identifier (com.*.AppIdStandalone).
- Log shows iOS and com.*.AppIdStandalone.

Expected result:
- Log shows iOS and com.*.AppIdIOS.

Workaround:
- Set the active build target to iOS through the Editor before launching the script.

Reproduced with:
5.5.0f1, 5.6.2p2, 2017.1.0f3

Not reproducible with:
2017.2.0b2

Note:
- Fixed in 2017.2, but it should be backported to 5.6. There was no case for this issue in the fogbugz.