First of all, if you want it clean coming out it has to be clean going in. Traces of oil, grease and other soils become quite visible after the high temp bake.
Secondly, vacuum furnaces are different. We have diffusion pumps on ours, and they get to 10^-3 or 10^-4 Torr readily. We don't have any problem with discoloration. Our LA facility has vacuum furnaces with only mechanical pumps, and theirs gets down to 10^-1 Torr. It's not surprising they see more discoloration than we do.
Oh, and to put in a shameless plug, AMS 2769 is a specification on vacuum heat treatment, so it's a useful reference document when dealing with supplier-purchaser issues. But what's best about it is the charts of metal vapor pressures in the back. They make it easy to explain to folks why we have chromium deposits on the cooler regions of our furnace interior.