There is a school of thought on this which, now I think about it, seems to me to be misguided. The school of thought is - When you have a longer lens than my 100-400, in order to maintain balance the camera body is positioned further back, behind the head. When you want to aim (very) high for an overhead BIF or the moon, for example, with the U orientation the body will hit the head and prevent you going as high as you might like. By inverting the "yoke" you gain some height to the system and a bit more room to swing the camera higher.
My issue with this is that the camera/lens needs to pivot about the centre of gravity, and as well as fore/aft balance adjustment you also need up/down balance adjustment, so that the equilibrium is not upset as you tilt the system. What that basically means is that the camera/lens need to be at the same height whether suspended from above or supported from below. However, when you place the yoke at the top, you are moving more of the mass upwards, which means that the camera/lens will actually have to sit a little lower in order to maintain vertical balance. Thus the intended purpose of suspending from above is actually self-defeating.
Now, when using a scope, which is relatively short and light, compared to a 1D3, flash and 600/4, by inverting the "U", as I said above, you will actually end up with the scope sitting a little lower, because the mass of the "U" is now above. That could be an advantage when using an angled eyepiece, as the scope will be at a better height for comfortable viewing without needing the tripod legs to be collapsed an inch or two.
As far as one configuration being easier to move, I don't see that at all. If your system is perfectly balanced, which is the aim, then it should be equally easy one way or the other.
I think the benefit, if any, of inverted configuration for photographers might come if/when you find you can't get satisfactory balance in the conventional "U" shape. Your height adjustment is limited to three pre-drilled holes. Thus height adjustment is a little crude and you may not be able to find perfect balance with the "U" shape. It may be that by inverting the yoke the weight distribution is altered and you may find that you can get a better balance, or very close. This is where I can see the Wimberley system offering a benefit, where it appears that you have the ability for infinite height adjustment with a sliding system rather than a series of holes.
EDIT : Actually, having taken another look at the image above, it might also be the case that the inverted "U" provides a little more space beside the lens, which might make access to lens switches easier, depending upon whereabouts they are positioned. So far I am more than happy with the more conventional "U" configuration. As the attached picture shows, I have plenty of access to switches and the camera is well clear of hitting anything, even if rotated to vertical. Maybe other lens configurations will be more problematic.
EDIT 2 : I did try setting it up overhead as well but found no benefit, and in fact it was a little harder to get close to perfect balance with the "U" inverted. On a different combination of camera/lens/flash etc. the results might well end up reversed. Also, as I have added the
Manfrotto 323 QR adapter, it happens to be a bit easier to fit and release the camera with things the way I have them, with gravity assistance when fitting the camera.