Turns out they do just flame anneal the crack and then by pulsing air into the vessel work the crack out. Afterwards they condition it in an kiln to relieve any aquired stress.
Windscreen cracks are different and are simply filled with an epoxy resin.
I found an interesting post on the topic here by Zan Divine http://www.sciencemadness.org/talk/viewthread.php?tid=18619
Approach the star crack with a soft, medium warm oxy-fuel gas flame so as not to cause it to propagate. Move in circles around the star slowly closing in on it.
Increase the flame temperature until you have a well-defined inner cone about 1/2 to 3/4" long.
Focus on the star now. Heat it until the glass begins to sag inward about a mm or so. Don’t let the glass become too fluid to control. Easy does it. By gently puffing on a rubber tube connected to the flask joint, push the glass outward by a mm or two. The idea is to make the star look like a slowly pulsing lump. This works the glass and causes the crack to fuse. This cycle is done 10 or 12 times and then the shape is adjusted by final puffs as you cool the glass just enough so it stay put.
Slightly, and in gradual degrees, cut down on the oxygen while playing the flame in circles around the repair. Over 3-5 min gradually cut off the oxygen. Eventually, play the yellow gas flame over the area laying down a thick sooty layer. This is called flame annealing and, for small repairs not near strained areas, it is quite good.
Let it cool, wipe it off, good to go. You will almost always see a very very slight mark where the glass fused. Microbubbles. Not a real concern.”