Closing a scene behaves differently depending on whether you use the shortcut or not.

### Tested versions

v3.6.beta3.official [21ab700f2]

### System information

w10 64

### Issue description

Watch the video:

- When I close a scene using the shortcut CTRL + SHIFT + W the scene is saved even if it has no changes.

- When I close the scene directly with the mouse, the scene closes quickly without saving as there are no changes to the scene.

Do not take into account the size of the scene or the elements that appear in it, this happens even with small scenes.

https://github.com/godotengine/godot/assets/19652075/df997160-436f-4f9d-a547-735f625dbbb1

### Steps to reproduce

There will be a scene.
Close the scene using the shortcut CTRL + SHIFT + W
There will be another scene.
Close it using the mouse.

### Minimal reproduction project (MRP)

...

Start by reproducing the scene-close behavior in the Godot editor on Windows, comparing CTRL + SHIFT + W with closing through the mouse on an unchanged scene. Trace the two close entry points and verify that both handle unchanged scenes consistently without unnecessary saving.

Written by the indexing model from the issue text.