This isn't to do with renaming qualifiers, but beware that using alpha channels in the custom qualifier icons is problematic. They look good in the icon editor, but then they end up screwed up in the actual MFA (eg. object properties, events). Transparent areas become solid black, for example, or other glitchy artifacts.
I've tried PNG32s, PNG8s with translucency (I didn't even know this was a thing until today) and PNG8s with binary transparency, and none of them work. Sometimes it appears to import the alpha channel, but then you see solid pixels in the MFA. GIFs seem to work, though they only have binary transparency, which doesn't look great in many cases.
I also managed to get a working alpha channel by importing a PNG8 with a solid background and using the "choose transparent color" feature when importing in Fusion. Even this method didn't work with a normal PNG32 - Fusion doesn't seem to be able to read the colors correctly on PNG32s when importing the qualifier icons, so you'll create an icon with a #000000 background, for example, and tell Fusion that #000000 should be transparent, but it'll import the black pixels as black anyway.
The weird thing is that the whole icon importing experience looks and feels pretty much just like the normal graphic importing experience in Fusion (eg. importing into active objects), which has none of these problems.
Anyway, I've resigned myself to just using white backgrounds on all my icons, and that works pretty well. The white edges are visible a little bit (on certain parts of the interface more than others), and for some reason Fusion changes them from pure white to a slightly greenish white, but these are minor issues. In regular use you don't notice.