This thread will probably go on with opinions from both sides.
I am no expert, but I believe that there a couple of pieces to this. The spacer cap and the compression plug. I think it is the compression plug that plays a major role in supporting a carbon steerer where the stem is attached. The length and location is important so that the stem doesn't crush the steerer. If leaving it flush prevents proper positioning of the compression plug, there could be a problem, likewise adding a spacer could do the same.
There are tons of threads on this out there. This video is quite interesting, especially towards the end, as it shows the impact of the compression plug on the OD of a carbon steerer that, for me, is pretty eye opening.
John