For the record, cyan (color 247) isn't really transparent, most wad editors just interpret it as such.
There are two formats of graphics SRB2 (and Doom) uses. One is used for flats. The other is used for everything else.
Flats are defined very specifically. They have to be square, their dimensions have to be powers of two, and every pixel is opaque. This is why SRB2's transparent flats aren't really transparent: there's a specific routine that skips drawing cyan pixels on translucent FOFs.
The other graphics format is a bit more dynamic. The dimensions can be whatever you want, but with a maximum of 255 pixels vertically. The best part, though, there can be transparent pixels.
Since Doom already uses a full 256 color palette, there's no room left to add a "transparent" color to image files in order to allow image editing programs to emulate the "transparent pixel" aspect of Doom graphic lumps. So what people decided to do was replace color 247 with transparent. Color 247 just so happens to be a duplicate color (pure black), so every possible Doom graphic can be represented with this color palette.
The problem arises when WAD editor programmers start hardcoding color 247 to be converted to transparent. Knowledge among users is lost and people begin to not know how stuff actually works. In reality, you CAN have a texture/sprite use the cyan color in SRB2, but most WAD editors either won't let you or make it obscenely hard. DeePsea is an example of an editor where you can just go into the options menu and set the working transparent color. You could set it to something which isn't in SRB2 at all (like a violet tone), and then import true-color bitmaps with the violet color in place of transparent pixels and DeePsea will do everything correctly and keep cyan where cyan's supposed to be.
