### 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)

ERR_FAIL_COND_MSG(!props.has(p_name), "Request for nonexistent project setting: " + p_name + ".");
#ifdef DEBUG_METHODS_ENABLED
	props[p_name].ignore_value_in_docs = p_ignore;
#endif
}
bool ProjectSettings::get_ignore_value_in_docs(const String &p_name) const {
	ERR_FAIL_COND_V_MSG(!props.has(p_name), false, "Request for nonexistent project setting: " + p_name + ".");
#ifdef DEBUG_METHODS_ENABLED
	return props[p_name].ignore_value_in_docs;
#else
	return false;
#endif
}
String ProjectSettings::globalize_path(const String &p_path) const {
	if (p_path.begins_with("res://")) {
		if (!resource_path.is_empty()) {
			return p_path.replace("res:/", resource_path);
		}
		return p_path.replace("res://", "");
	} else if (p_path.begins_with("user://")) {
		String data_dir = OS::get_singleton()->get_user_data_dir();
		if (!data_dir.is_empty()) {
			return p_path.replace("user:/", data_dir);
		}
		return p_path.replace("user://", "");
	}
	return p_path;
}
bool ProjectSettings::_set(const StringName &p_name, const Variant &p_value) {