### Godot version

v4.0.beta10.official [d0398f62f]

### System information

Windows 11

### Issue description

Using a custom "Project Settings Override" file causes Godot to immediately modify main project file (`.godot`) on startup.

The attached project demonstrates this issue. The project has the following 3 things defined:

1. Window display mode is set to "Exclusive Fullscreen" (`window/size/mode=4`) in main project file.
2. Custom project override file is set to "res://override.cfg" (`config/project_settings_override`).
3. Inside "res://override.cfg" window display mode is set to "Windowed" (`window/size/mode=0`).

Opening this project will immediately modify main project file to have "Windowed" display mode (discarding original "Exclusive Fullscreen" setting).

### Steps to reproduce

1. Open example project.
2. Go to Project Settings -> Display -> Window -> Mode.
3. Expected option is "Exclusive Fullscreen", actual result is "Windowed".

### Minimal reproduction project

[override-issue.zip](https://github.com/godotengine/godot/files/10312624/override-issue.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() {