### 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)

Error err;
	Ref<FileAccess> f = FileAccess::open(p_path, FileAccess::READ, &err);
	if (err != OK) {
		return err;
	}
	uint8_t hdr[4];
	f->get_buffer(hdr, 4);
	ERR_FAIL_COND_V_MSG((hdr[0] != 'E' || hdr[1] != 'C' || hdr[2] != 'F' || hdr[3] != 'G'), ERR_FILE_CORRUPT, "Corrupted header in binary project.binary (not ECFG).");
	uint32_t count = f->get_32();
	for (uint32_t i = 0; i < count; i++) {
		uint32_t slen = f->get_32();
		CharString cs;
		cs.resize(slen + 1);
		cs[slen] = 0;
		f->get_buffer((uint8_t *)cs.ptr(), slen);
		String key;
		key.parse_utf8(cs.ptr());
		uint32_t vlen = f->get_32();
		Vector<uint8_t> d;
		d.resize(vlen);
		f->get_buffer(d.ptrw(), vlen);
		Variant value;
		err = decode_variant(value, d.ptr(), d.size(), nullptr, true);
		ERR_CONTINUE_MSG(err != OK, "Error decoding property: " + key + ".");
		set(key, value);
	}
	return OK;
}
Error ProjectSettings::_load_settings_text(const String &p_path) {