### 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)
Error err = _setup(p_path, p_main_pack, p_upwards, p_ignore_override);
	if (err == OK) {
		String custom_settings = GLOBAL_GET("application/config/project_settings_override");
		if (!custom_settings.is_empty()) {
			_load_settings_text(custom_settings);
		}
	}
	
	bool use_hidden_directory = GLOBAL_GET("application/config/use_hidden_project_data_directory");
	project_data_dir_name = (use_hidden_directory ? "." : "") + PROJECT_DATA_DIR_NAME_SUFFIX;
	
	Compression::zstd_long_distance_matching = GLOBAL_GET("compression/formats/zstd/long_distance_matching");
	Compression::zstd_level = GLOBAL_GET("compression/formats/zstd/compression_level");
	Compression::zstd_window_log_size = GLOBAL_GET("compression/formats/zstd/window_log_size");
	Compression::zlib_level = GLOBAL_GET("compression/formats/zlib/compression_level");
	Compression::gzip_level = GLOBAL_GET("compression/formats/gzip/compression_level");
	project_loaded = err == OK;
	return err;
}
bool ProjectSettings::has_setting(String p_var) const {
	_THREAD_SAFE_METHOD_
	return props.has(p_var);
}
Error ProjectSettings::_load_settings_binary(const String &p_path) {