A vacuum insulated glass (VIG) window assembly and method for making same is provided in which a variation in the final edge seal height is preferably 0.20 mm or less, more preferably about 0.15 mm or less. Controlling final edge seal height variations substantially reduces breakage of the glass substrates of the VIG window assembly during vacuum pump-down of the cavity between the glass substrates. Edge seal height variation may be controlled, for example, by controlling initial dispensing of green frit material, controlling temperature variations during firing, and/or controlling cycle times during firing.