As of now "Top" has advantage when using mixed ground and air army - if it was under units, then either:
- air units healths would mess with all the ground, if health is shown at the ground point of each unit
- or, health will confuse positions for air and ground, because for ground it would be where they are, but for air it would be way above their actual map point
Also remember, the main reason why it isn't as clear as BW is that this is not 2D, depending on terrains and angles it is expected for healths to overlap more often. The cure is to get used to controlling the camera when needed.
As for bottom/top customizations - I actually prefer this to be chosen as some standard, so that it doesn't cause confusion every now and then, if you view completely different configuration. You should understand that excessive customization is not always a good thing.