Reproduction steps:
1. Open the attached project "ScenedTest"
2. Right-click "Scenes/DefaultScene" and select "Create/Scene Template From Scene"
3. Press Ctrl+N
4. Create a new scene from the created template

Expected result: one of the cubes is green, the other is red
Actual result: both cubes are green

Reproducible with: 2022.3.5f1, 2023.1.5f1, 2023.2.0b2
Could not test with: 2021.3.29f1 (Save SceneTemplate has failed. Asset path error: 'DefaultScene.unity' is not valid: Incorrect extension. Required extension is: '.scenetemplate’.)

Reproducible on: macOS 13.4.1 (Intel), Windows 10 (user’s)

Note: there are two "CubeMaterial" materials, one in "FolderWithGreenMaterial" folder, and one in "FolderWithRedMaterial"