Hello All,
The remaining colour is indeed grain structure and carbon and inclusion "Ribbons" uncovered by the loss of iron due to corrosion, unfortunately there really is only one way to get that "fresh machined finish" and I'm sure you've already guessed what that is, when I was studying metallurgy I worked in a steelworks testing lab doing photo etching and all sorts, and the upshot is that metals are far from homogenious regular materials. when the surface is machined often the very top layer of atoms are "smeared across the face leaving a kind of burnishing on the surface which is that shiney face from machining, once you etch it with acid or electrolytic processes that surface is gone and the only way to get it back is to reburnish it. Sorry to be the bearer of bad news there.
But, using never seize is absolutely the right thing to do, never seize isn't alluminium as some have mentioned but rather it is usually nickel based, the nickel is ground superfine and is so fine that it will get into the smallest porosity, the oil will be displaced when the buffing cloth burnishes the surface and once the oil is pushed out the nickel will no longer be mobile, if you find a never seize compound that uses aluminium give it a miss as it will probably cause galling rather than prevent it, the aluminium will oxidise quickly making an abrasive, actually the second toughest behind diamond, and as you probably know abrasives are not good lubricants. the burnishing of nickel particles will resemble the burnished steel from machining, and if the mark you are covering is a porosity defect, which it most likely is, the mating parts will not reach into the pits to scrape out the nickel, so the finish will be relatively permanent, and when it wears off just do it again, with each application it will last longer and longer.
I hope this helps,
Best regards
Rick