It boils down to personal preference. Most people don't want to mess with macros at all, and therefore most profiles you see people posting will have no custom WoW macros. If you're going to set up WoW Macros though, setting up through ISBoxer definitely carries the advantages over setting up in-game.
I'm rebuilding my Pro configuration right now for my WoW Paladins, and currently I'm not using WoW Macros. I'm having ISBoxer press the same buttons in the game that I would use when playing solo. However, the problem with this method is that if I rearrange my Action Bars, then I also have to update my ISBoxer profile to match the new buttons.
But, the same problem exists once in a while for WoW Macros too. For example, the "CLS" configuration contained a WoW Macro for every ability for every class. When Cataclysm hit, they changed many of those abilities, so tons of macros had to be changed or removed.
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