Regarding how the crossover could have come about in-universe, I have a theory that the two realities of the Trekverse and the Whoniverse were somehow temporarily merged together to form a hybrid reality; this would explain how Whoniverse species like the Judoon and Slitheen could suddenly exist in the Trek galaxy.
The story suggests that the universes are merging early on (issues 3 and 4). However, the story then goes in a different direction and suggests that they're two wholly separate universes; the Cybermen's plan doesn't make sense otherwise.
I take away from Picard's trip in the TARDIS that the Judoon and the Slitheen naturally exist in the Star Trek
universe. Which leads me to wonder if there's a Skaro in the Star Trek
universe. And, if so, did Skaro avoid the thousand years of war? Could Davros be hailed around the Federation as a scientist and healer?