Underground belts and trains should also work. The teleporter has middle area of something like 5x4 tiles (read ingame description). Outside this area is 1 tile border that gets damaged. There is also the concept, that rails are specially built, so they don't get damaged.
As for automation, latches should help. Also I think belt reading has a checkbox to "flash" a circuit signal for a moment. So for example when chests are filled, overflow is put on a belt, which triggers a signal only once when items first appear.