### Godot version

v4.0.2.stable.official [7a0977ce2]

### System information

Windows 10

### Issue description

The settings found in **application/config/project_settings_override** end up being written to the `res://project.godot` every time the editor is started.

I find this inconvenient, `res://project.godot` is always on the changelist in git because of this.

I think it would be better if settings with the same value as found in **application/config/project_settings_override** were persisted in `res://project.godot` **only** when set by the "editor interface" or "by code" and not by the "merge" that happens at the start of the editor.

### Steps to reproduce

1. Before opening the MRP in the editor, note **window/size/mode** value within `res://project.godot`;
2. Now open it in the editor and check the `res://project.godot`, notice that **window/size/mode** was changed by the contents of `res://project_override.cfg` (which is the **application/config/project_settings_override** file).

### Minimal reproduction project

[Projects Override Merging Into Project Godot.zip](https://github.com/godotengine/godot/files/11555239/Projects.Override.Merging.Into.Project.Godot.zip)
bool found = _load_resource_pack(exec_path);
		
		
		String exec_dir = exec_path.get_base_dir();
		String exec_filename = exec_path.get_file();
		String exec_basename = exec_filename.get_basename();
		
		
		
		
#ifdef MACOS_ENABLED
		if (!found) {
			
			found = _load_resource_pack(OS::get_singleton()->get_bundle_resource_dir().path_join(exec_basename + ".pck")) || _load_resource_pack(OS::get_singleton()->get_bundle_resource_dir().path_join(exec_filename + ".pck"));
		}
#endif
		if (!found) {
			
			
			found = _load_resource_pack(exec_dir.path_join(exec_basename + ".pck")) || _load_resource_pack(exec_dir.path_join(exec_filename + ".pck"));
		}
		if (!found) {
			
			
			found = _load_resource_pack(exec_basename + ".pck") || _load_resource_pack(exec_filename + ".pck");
		}