People buying cheap pre-built computers typically aren't the most knowledgeable customers. I'm willing to bet the asking price for the AMD systems was higher because they were being marketed as having more cores or higher clock speeds. The uninformed consumer sees 4 "cores" and more GHz and somehow thinks it must be more valuable because it has more, bigger numbers. Companies can sell based on perceived value (It's why companies like Apple and Nvidia can command far higher prices for products that are similar or not substantially better than alternatives for their price) not just some more objective measure of value.
I don't know if Ryzen does well in the low-cost pre-built market though. Even though they might sell their product for less than an i3, the i3 still has integrated graphics whereas using a Ryzen chip means getting an low-end discrete GPU. Maybe AMD is happy to flog some Polaris 11 or even some old 28nm leftovers to the OEMs at a cost where it makes financial sense over an i3, but it's easier from a manufacturing point of view to use the integrated solution. Raven Ridge might change this dynamic, but we'll have to wait a while for that.