Note I have not looked at or modified the Morphology code in a long time. It was (and should be) correct.
Wish I had more time but I don't any more
Before the change to morphology.. Blur and Gaussian blur did not handle transparency (alpha blending), unless you specifically included it in a non-default -channel setting of RGBA
That was nonsensical, as it meant that normally invisible transparent colors would take part of the blur.
After the change (if the code is working right) Alpha blending (correct handling of transparent colors) would be enabled BY default. that is Image has an alpha channel enabled, and the default 'Sync' channel flag was present.
To prevent alpha blending (just blur channels as if they were completely separate grayscale images) you can do any of the following..
1/ turn of alpha using -alpha off
2/ Make alpha opauqe using -alpha opaque - both of which results in transparency color blending
3/ replace transparency with a fixed color using -alpha remove
See IM examples, Removing Transparency from Images http://www.imagemagick.org/Usage/masking/#alpha_remove
4/ Set channels so as to remove the 'sync' flag (IE enable channel selection)
using -channel RGBA (alpha and cloor channels blurred with out blending making more hidden color visible)
using -channel RGB (does not modify alpha, though hidden colors is still blurred in result)
This is equivelent to using a 'Write Mask'
5/ Use a "Read Mask"
That last IS DIFFERENT. It means simply do not involve any 'masked' color in the bluring process.
That is do not read those pixels when blurring the image! this is NOT easy to do in IMv6.
and is NOT the same as a write mask.
See IM Examples, Read Masks http://www.imagemagick.org/Usage/masking/#read_mask