I see no issue using the Mako saddles. I had this same set up on my 2007 Subaru and my 2010 Hobie Outback.
I also bought the Yakima "show boat rear roller" to protect the rear hatch spoiler while loading. It worked very well.
Make sure the Hobie Outback is not over tightened to the Mako saddles/crossbars. That will prevent any possibility of hull deformation in the hot sun.
I used both a bow and stern safety line for additional security at highway speeds.
The bow line was fed through a 2' long pool noodle to protect the hood.
This is an older photo (7 years ago with a 8.5# Steelhead size trout) and you can see part of the Yakima equipment.