I didn't get the impression that they consider the Console API in itself a flaw. An API for this is much more robust than an in-band text API that's part of your output. For example, no Windows console application has to even think about whether printing a user-provided string can be a problem. They do note that it's an impediment for porting software to Windows, as well as the problem that the API isn't able to be implemented by any other application, e.g. ConEmu. Those applications have to rely on scraping a hidden console window to work instead of just being an alternative console implementation.

I read it not so much as a testament to the perceived superiority of the Unix model, but rather that with WSL users expect certain things to work more Unix-like, just that they don't work like that right now.