How to reproduce:
1. Open the attached "SaveSceneInPackage.zip" project
2. Open a new Scene
3. Right-click on the Scene and select Save Scene as
4. Navigate to Packages/MyAssetPackage/Runtime
5. Type in the File name and click save
6. Observe the warning window

Expected result: Scene is saved in the package
Actual result: Warning that scene needs to be saved in the Assets folder

Reproducible with: 2018.4.27f1, 2019.4.10f1, 2020.1.5f1, 2020.2.0b3

Notes:
1. After saving the Scene to the Assets folder, it is allowed to drag it to the Package that is in the project
2. Saving assets outside of the Assets folder is also not allowed. When extracting materials to the Packages folder "Couldn't create asset file" error is thrown in the Console window