Hi Alex,
to IIS!
I agree with Glen - roof racks is not a good place to transport such a large Newtonian! It will cop a massive buffeting from the wind as you hurtle down the M4 at 110km/hr! The vibrations the scope will be subjected to are bad news! Though not heavy, it is a BIG volume and not make for safe driving, particularly at speed. Won't help fuel consumption either.
If you cannot fit it across the back seat of your car, could you drop the back support of the front passenger seat and put the scope long the passenger side of the car, from glove box to back seat? This is how I used to transport my big 17.5" dob when it was a solid tube instrument (see pic below). That was not a scope to stick up on roof racks!
I also had a 12" f/5 solid tube dob at one time. I never even contemplated putting it up on roof racks!
Maybe if we knew the sort of car you have we'd also be able to give you better advice. Roof racks is not a place to be carrying a big dob, like a 12". It will severely compromise the safety of the primary mirror in its cell - it is heavy and the clips that hold it in place are not designed to deal with the mirror in the position roof racks will put it along with the buffeting the scope will get - case or no case!
Cheers,
Alex.