Reproduction steps:
1. Open the attached project "BuildNotStripped"
2. Open “Assets/Scene/Game.unity“ Scene
3. Open Build Settings (File > Build Settings)
4. Set Platform to Dedicated Server
5. Build the project
6. Observe build size (right-click on the build folder > properties)
7. Select the “Environment“ Subscene reference in the Hierarchy window
8. Set Scene Asset to “Environment“ in “Sub Scene (Script)“ in the Inspector window
9. Repeat steps 4-6

Expected result: Both builds are the same size
Actual result: Graphic assets are not stripped when the scene is saved as a reference

Reproducible with: 1.0.17, 1.1.0-exp.1 (2022.3.12f1)
Couldn’t test with: 1.0.8 (2022.3.12f1) - “error CS1061: 'EntitySceneReference' does not contain a definition for 'IsReferenceValid' and no accessible extension method 'IsReferenceValid' accepting a first argument of type 'EntitySceneReference' could be found“

Reproducible on: Windows 10
Not reproducible on: No other environment tested