The whole point of the pin & weld method is that all of the welding takes place on the muzzle extension (FS, comp, brake, etc.), and NOT on the barrel.  You don't want to heat the barrel up that much, as it will stress the barrel and could affect accuracy.  The pin & weld allows a small torch head to be used and to only heat up a small area of the muzzle extension.

Certainly, that area will need to be refinished.

Oh, BTW, the "high-speed" way to do this is to use a laser welder to weld the pin in place.  Laser welders super-heat a very tiny area, so no refinishing is needed.  Of course, not many places can do this.

-Troy