Themes cannot be installed into the Stacks folder

If a theme is not inside the Themes folder, you see it in the theme library, but it's not truly loaded. The settings for the Sample Theme will be displayed instead. It also does not show up in the Primary Theme dropdown list in the Site Settings.

I was hoping to ship this inside of my existing Foundation 6 stacks as an update. This seemed to be the most seamless way to get users to transition to Stacks 6.

You can put any theme directly into the Stacks folder and see this behavior. But I sent you a copy of the Foundation 6 stacks with the theme built-in.