Semi-transperancy for most blocks does not work when using a texture pack

when trying to create a custom texture for the glass block it does not let me make any pixel on it semi-transparent. This is weird because it's stained variant supports these semi-transparent pixels. I wonder if this in intended or not?

*All the blocks in the image below use the same texture but they all display differently and only the stained glass works properly. Hotbar textures work though.