"Is it safe to assume that users who want to use a "dark filter" do not a scope cover, right?"
I do have a cover for my scope. I just like to use the dark filter as an extra layer of protection against light leaks, especially if/when I try taking darks during the daytime.
As a hack, you could probably schedule a single light photo using the dark filter before scheduling the darks. That should ensure the filter wheel is in the correct position for the darks.