I didn't know there were partially open source RISC-V. I might have missed it in the article, but what was the reason for having some parts closed source?

It’s not the RISC-V core itself, it’s just some of the surrounding architecture to support the CPU, to turn it into a SOC. So the USB drivers, the AXI memory interfaces, and the analog components, like PLLs for generating clocks, or even the IO pad drivers. These components take the fully open RISC-V core which works in a simulator and makes it work like a normal physical chip would.