### 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)
#include "project_settings.h"
#include "core/core_bind.h" 
#include "core/core_string_names.h"
#include "core/input/input_map.h"
#include "core/io/config_file.h"
#include "core/io/dir_access.h"
#include "core/io/file_access.h"
#include "core/io/file_access_pack.h"
#include "core/io/marshalls.h"
#include "core/os/keyboard.h"
#include "core/variant/typed_array.h"
#include "core/variant/variant_parser.h"
#include "core/version.h"
#ifdef TOOLS_ENABLED
#include "modules/modules_enabled.gen.h" 
#endif 
const String ProjectSettings::PROJECT_DATA_DIR_NAME_SUFFIX = "godot";
ProjectSettings *ProjectSettings::singleton = nullptr;
ProjectSettings *ProjectSettings::get_singleton() {