I took apart my shimano m770 front and rear hubs, and removed both (!!) cones on each axle. When reassembling everything I ran into the issue of re-centering the axles (so that the rims run in the middle of the fork/frame). What I did was centering the wheels by eye as good as I could, but I'm sure I'm still 1-2mm off center. What I wonder is, if this will cause any problems (I use rim breaks) or if it's totally fine?
(Re-worked this answer completely because I forgot at first that M770 hubs have nonstandard axles).
First of all, under almost all circumstances, you should leave the integrated cone/axle unit of hubs like this alone, other than maybe the fringe case of making one good one out of two identical bad ones or something weird like that.
I'm assuming it's clear that you must find some way of getting the drive side cone permanently re-attached to the axle, because it doesn't mechanically lock in place like a standard axle. Epoxy in the threads, etc.
The approach I would take here is try to find witness marks on at least one of the cones or the axle that show you about what the original thread engagement was on at least one piece of it when the drive side cone was originally affixed to the axle. Combine that piece of information with the knowledge that the over-locknut dimension is 135mm and you should be able to make everything fall into place.
Alternatively, if Shimano's EV diagrams were 100% to scale, down to the representation of the thread pitch, counting threads on the diagram would get you there pretty closely. I suspect they might be that accurate but I'm not really sure.
But to answer the specific question, nothing is getting put out of alignment in terms of the wheel/rim relative to the frame or brakes if you eyeballed it when putting it back together. It just means that one piece has a little more thread engagement and the other has that much less. In extreme situations that could present its own issues in terms of the parts being properly secured and the threads staying in good shape, and hypothetically as a result of the strong, full-thickness part of the axle being in the right spot, but in this situation 1mm probably won't make any difference.
Quick release axle or bolt-on? If it's bolt on, you should be fine to just eyeball it. Quick release should be as even as possible, because if it's too thick on one side, the quick release will not properly close on that side.