Personally, for me, it is MUCH easier to go into the "app" I am working on and find ALL my prefixes already defined there, and it is MUCH easier to add them into that area.
As I stated before, there are some areas that I use the SAME prefix for different add-ons. But in each add-on they are styled differently. I really don't see how that can easily be done without having multiple listings of a Prefix in a "master list" with the associated confusion that would entail unless one added the add-on as a prefix/suffix to the CSS styling, such as prefix_general_XFRM
and prefix_general_SC
and prefix_general_CAS
and so on and so on.
Can it be done? Probably?
Does it necessarily need to be done? Doubtful as it WOULD interfere with an existing workflow.