Either version is the "flat" version. The difference between the two "eyes" is so small, you wouldn't be able to detect it watching the film flat. This is why initially 2-D engagements weren't until the end of the 3-D run, because that way the prints could be split up and sent to the second-run houses flat.

The side that is used for transfer, TV prints, 16mm prints, etc. is usually dictated on how the camera rig is oriented and what side of the film the emulsion ends up lying on.