To reproduce:
1. Open attached project "iosCheckbox7.zip"
2. Make sure that Automatically Sign is enabled in Player settings
3. Build for iOS
4. Open the built Xcode project
5. Observe as Automatically Sign is enabled
6. Close the editor
7. Run Unity in batch mode with " sudo /Applications/Unity/Unity.app/Contents/MacOS/Unity -quit -batchmode -logFile output.txt -projectPath *project path* -executeMethod BuildUnityPlayer.buildIOS
8. In Finder open iosCheckbox7 > ios > Unity-iPhone.xcodeproj
9 Observe as Automatically Sign is disabled

Expected: Automatically Sign is enabled doing batch mode build
Actual: Automatically Sign is disabled doing a batch mode build, even though it is enabled after building it from Editor

Reproduced on:
2018.1.0a2 2018.1.9f2 2018.3.0a1 2018.4.4f1 2019.1.11f1 2019.2.0b10 2019.3.0a10

Not reproduced on:
2017.4.30f1 2018.1.0a1

Regression introduced in:
2018.1.0a2