Well, quick update.
I finished the rest of the car, then went back to work on the roof.
Another round of Fine Machine Polish, then the appropriate amount of MSS and the scratches were gone.
I've been at this since 9am, so it's gonna cure overnight before I move on to the Brilliant Glaze and finally, Americana.
Thanks for all the replies. I am sure you can understand how relieved I was to hear they weren't permanent marks!
BTW- It's a new Ford Focus ST. Performance Blue <- their name, not mine. Although I am sure it's good for another 20HP.