Well, from an Aeronautical Engineering viewpoint, there is a longitudinal line running down the fuselage that is usually the physical reference. By raising the wing, you're changing the angle of incidence of the wing. This wasn't something new either. The XB-51 was able to change the angle of incidence of it's wing as well and there were other designs that explored this as well, before the F-8 came along. Such as the original design of the Grumman Jaguar, before they switched the design to a swing wing.
So the short answer is, you're neither raising the wing or lowering the fuselage. You're changing the angle of incidence of the wing, allowing the wing to have a higher alpha without raising the nose as high as would be required if it were fixed. This allows the pilot to maintain good visibility on approach and also allows a shorter landing gear due to having a lower tail scrape angle, which also reduces weight and improves performance.
Of course, the weight of the system that changes the angle of incidence adds weight, which lowers all up performance. But, as with everything in aircraft design, there's always a trade-off.