I made a skin in a modelling program and it showed it transparent, but now it seems you cant do that, it has black in the transparent parts now.
This is true, the inner layers cannot have transparencies.
The modeling program only displays it as transparent because there's nothing to render.
There might even be an option to set it as black just so you can see the different surfaces.
In Minecraft, however, anything that isn't a solid color will render as black.
Now, on the outer layers anything can be transparent, or any value between solid and invisible.
I also didn't think it was implemented because people can exploit this; use it as a cheat on servers and stuff if they were to be totally invisible or semi-transparent.