As I understand it Zen is already a Soc. It has sata and usb built in. No chipset means that you free up a x4 PCIe slot. So for example if you want a 10 GbE instead of GbE you can do that. Add a usb hub and you can plug all low speed peripherals into a single USB port.
Ryzen was built as an SoC for efficiency purposes for those devices, and you are right in theory it can be plugged into a "naked" board and function (although how "naked" it can be is up for debate since the concept has not yet been proven). But at this point for the high end size of the chips the uses for that are minimal. Aside from a few niche users nobody is going to want that, they are going to want the additional PCIe slots, etc that a chipset provides.
Maybe when the R3 comes out you will see some sort of SoC motherboard for low power setups. But for large high end chips thats just not what people are looking for.