Chris,
Option #1 (fore/aft) is how I use my StackShot and RRS clamp. Used in this way you can connect your camera via the lens collar. This will enable you to alter camera orientation to either landscape or portrait depending on the composition.
I tend to use a bellows with an Arca Swiss dovetail base. Option #1 is the applicable configuration for such equipment.
Option #2 (side to side) For landscape or portrait orientation you could use an 'L' bracket attached directly to your camera, but such a bracket would be more limited with regard to possible orientation options.
Besides, any adapter or tools that can convert the QR Clamp orientation without unscrew the plate?
A bi-directional, camera specific quick release plate will allow you to mount the camera body directly in either direction fore/aft or side to side (should you wish to do so) without the need to alter the clamp configuration.
There are additional alternatives/approaches for on-the-fly adjustments between fore/aft or side to side positioning such as the RRS PCL-1: Panning Clamp:
http://reallyrightstuff.com/ProductDesc.aspx?code=PCL-1 (there are 'clones' available, but the 'clone' I have is not as accurate as the original)
Which camera/lens combination are you currently intending to use?
I suggest working with Option #1 (fore/aft)
Craig
* edit added link