If both of your bodies where absolutely perfect, and the adjustments only affected the lenses, then I would think copying setting would be fine. However, it is possible that part of the adjustment is due to backfocusing issues in your body. Therefore, if you copied the settings from one camera to the other you may find they don't work.
What I would suggest is take one of your lenses, and mount it to your other camera. Manually do a MA to get it in focus. Check the setting to see if it matches your other camera. If the setting is the same as what you found on your other camera, I think it is safe to say that both bodies are spot on, and then I would just copy the settings for all of the lenses. If it is not, then it's reasonable to think that part of the problem lies in the body, and I would re-check with a second lens. If that lens doesn't match the setting from the first camera, then at that point I would just manually MA all my lenses on the second body.