First, just to be clear, I don't have anything to do with the writing of Carbonite or any other addon, so what I say in these forums is my opinion, not necessarily gospel. Second, I have been using Carbonite for a long time, and I think I have a pretty good idea how it works. That said...
By default, WoW has two maps: the large map and the minimap. They are completely different entities, and have different APIs. The Carbonite map is a replacement for the large Blizzard map. It has nothing to do, directly, with the minimap. It does have a "minimized" view, and therein, I think, lies the confusion. The minimized Carbonite map is not the minimap, nor is it a replacement for the minimap. In particular it does not use the minimap api - it uses the large map api, even when minimized. I think, but am not certain, that one thing it does do is to supress some icons (when minimized) simply to keep down the clutter.
The minimap may be merged with the Carbonite map, or it may be docked in the Carbonite map. Frankly, I'm not sure what the difference is between these two options, but certainly "docked" implies that it is still a separate object with a separate api. I suspect the same is true when the minimap is "merged", but I don't know. In any case, though, if you try to use the minimized Carbonite map, placed in a particular location, as the "minimap", if the minimap is merged with or docked in the Carbonite map, you will find when you enlarge the map that there is nothing in the particular location where you were keeping the minimized map. This is of course not the case in either the default Blizz interface or using Carbonite with the minimap not merged or docked - because as I said above they are compeletely separate objects. When you open the default Blizz map, the minimap is not affected. When you open the Carbonite map, the minimap is only affected if it is merged with or docked in the Carbonite map.
That's my understanding. If I'm wrong, perhaps Rythal can clarify where I'm wrong.
