There are two options for top-tube-holding racks- There are 'false top tubes' sold by some rack companies that are like a turnbuckle link between your saddle and stem, designed just for this application. They're easy to install and normally removed when riding, or...
Just put your bike on it and accept that it will be on an angle. Look around next time you are driving and about half of all bikes are canted significantly on their racks. It's not a big deal at all. I regularly carry my SO's step-through frame on an old Thule hitch-mount rack, and the front wheel is down by the bumper and the rear wheel is up in the rear window of the car. It has never been a problem.