I have a Texture2D that has some dynamic shapes colored into it and the background is transparent.
I call GetPixels() to get a section of pixels to modify, and basically just set all of their colors to Color.black;
Then I call SetPixels() on the textures and then use Apply().
The pixels that had color and were not transparent will change to black, but the background part that is transparent, I cannot make it any color it just stays transparent.