Sync helps some, as user snibgo mentioned earlier, but does not produce the same result. It leaves a slight black shadow whereas the old version does not.
Compare the attached images and also look at them with -alpha off to see why. The old version propogated the underlying image further outward so that the alpha channel did not blend it with some of the black surrounding. The newer code does not propagate the colors far enough and thus there is still some blending of partial transparency with the black that shows in the results. This likely due to improper alpha weighting or from a different alpha weighting method that is not as good as the old alpha weighting. This may have been an oversight on Anthony's part or a bug in his code.
Correct older versions of IM before 6.8.4.0 without sync results of command with and without alpha
im6840 convert colorcone.png -channel rgba -blur 0x5 cc2.png
Incorrect current version 6.8.7.10 with sync results of command with and without alpha
convert colorcone.png -channel rgba
,sync -blur 0x5 cc2.png
Original image:
If the current code is fixed to work the same with the sync flag added, then the -blur docs should explain that, since the sync flag was not needed to achieve the good results in older versions of IM. I suspect it was overlooked when the switch to the morphology blur was made and no one until now noticed the issue.