How to reproduce:
1. Open the attached “IN-88802” project
2. Build and run the project using the “TestProfile” profile
3. Observe the Scene
4. Open a command line interface and build the project using the command provided in the note below
5. Open the built project
6. Observe the Scene

Expected result: Both builds should display the same scene
Actual result: The first build displays the “GlobalScene” Scene while the second (command-line) build displays “ProfileScene” Scene

Reproducible with: 6000.0.27f1, 6000.1.0a4
Could not test with: 2021.3.46f1, 2022.3.52f1 (Build profiles do not exist)

Reproduced on: Windows 10 (User), Windows 11, macOS
Not reproduced on: No other environment tested

Note: Run this command from the <UnityEditorPath> directory where Unity.exe is located: {{Unity.exe -batchmode -quit -projectPath "<ProjectPath>" -activeBuildProfile "Assets/Settings/Build Profiles/TestProfile.asset" -build "<OutputPath>/MyProject.exe"}}