I'm reading between the lines, but it looks like the linux subsystem is using a separate file system. So you'll have the usual problems when using files from /mnt/c, but other files are mounted in a unixy file system of some sort. The Ubuntu file system is mounted onto your Windows subsystem at C:\Users\<user>\AppData\Local\Lxss\rootfs\, according to the article.
I'm guessing you are right. The usual problems with /mnt/c. I was wondering about rootfs being per user as well. On a server that may be a problem, but perhaps not on a laptop. It sounds like this is not meant to be the basis for production level deployments, but useful for development.