You are right. If you spend much time to adjust the table mechanically, you can get a nearly perfect orientation for your frame. Don't worry.
But it is absolutely not neccessary to do that, you can save that time, if you teach the frame.
It took me 3 tries by hand using my position values to reach the same coordinates if I move in the x or y. I jog my z to the same height and also using dial calipers to measure as close to the same spot as possible. And i was able to get 0, 0, 90
Don't understand this at all.
You should provide some pictures of your physical settings. And how you teached the User Frame.