As far as I am aware, the government can overrule the Scottish courts in the supreme Court.
This is more grandstanding. If they were serious, they would have gone to a court which has UK pertinence within the Union. Not a Scottish country court.
As this is Union law and not Scottish law, I would not expect the court of session to have durisdiction. Although it might try to rule anyway.
We have a few months for all these shenanigans to play out.