I'll have to look closer at the material but I think it's molded in color.

I had another idea that might work better then coloring the logo. Last year I made a trophy out of 5.7 Hemi engine parts. I had a trophy shop make me an etched aluminum label for the base. It only cost $5. I could have them make me something similar. Grind the rubber logo flat and affix the aluminum plate over the top. I could have the etching say "Black Edition". That might look nice. I might even be able to completely remove the logo and "hide" the wonky stitching with the plate.