### 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)

if (p_path.ends_with(".binary")) {
		return _load_settings_binary(p_path);
	}
	return _load_settings_text(p_path);
}
int ProjectSettings::get_order(const String &p_name) const {
	ERR_FAIL_COND_V_MSG(!props.has(p_name), -1, "Request for nonexistent project setting: " + p_name + ".");
	return props[p_name].order;
}
void ProjectSettings::set_order(const String &p_name, int p_order) {
	ERR_FAIL_COND_MSG(!props.has(p_name), "Request for nonexistent project setting: " + p_name + ".");
	props[p_name].order = p_order;
}
void ProjectSettings::set_builtin_order(const String &p_name) {
	ERR_FAIL_COND_MSG(!props.has(p_name), "Request for nonexistent project setting: " + p_name + ".");
	if (props[p_name].order >= NO_BUILTIN_ORDER_BASE) {
		props[p_name].order = last_builtin_order++;
	}
}
bool ProjectSettings::is_builtin_setting(const String &p_name) const {
	
	ERR_FAIL_COND_V_MSG(!props.has(p_name), true, "Request for nonexistent project setting: " + p_name + ".");
	return props[p_name].order < NO_BUILTIN_ORDER_BASE;
}
void ProjectSettings::clear(const String &p_name) {
	ERR_FAIL_COND_MSG(!props.has(p_name), "Request for nonexistent project setting: " + p_name + ".");
	props.erase(p_name);
}
Error ProjectSettings::save() {