Before the silica grains fuse, the spaces between grains are filled by atmospheric gases. When the grains fuse, those gasses are entrapped by the highly viscous melt. So the composition of the gas in the bubbles is roughly the same as the atmosphere inside the furnace, unless impurities in the silica (e.g. carbon) are released from the grains themselves.
Methods exist for removing the air from the walls of the crucible while the quartz is still molten, usually by drawing a vacuum through small holes in the mold.