Does Workshop Automation use Workshops?
Solution 1:
It sure does! The only thing it doesn't take into account is catnip refining. But since Workshops don't affect that anyways, there's no reason the automation should, either.
One thing to make note of, though, is that automation only kicks in at the beginning of spring, and only for a certain amount of your resources. So, it makes unattended gameplay more efficient, but not that efficient.