yep the shuttle cooler is a custom job along with the shuttle ITX motherboard, some of the newer cases are also now compatible with standard miniITX motherboards which make them a far better option than the older shuttles because you pay for that proprietary form factor.
For a cooler your best bet is to make/or have made a custom mounting kit, a back plate is nothing very complex, making a retention plate that can attach to your cooler is more complex, does depend on the cooler though.