Wow, Chris! I've been gone for 3 months and you've done a lot. I love your build. I'm fighting home deficiencies from winter storm that us Houstonian's aren't prepared for, and a drivetrain update on my GTO, otherwise I'd be doing similar things, like the latches and door rebuilds...
Your bed floor turned out great! My plan is what you still think you want to do... metal floor with bedliner, which I currently have. The liner the PO used was a cheap one, so it's flaking, and there's some rust that needs to be tackled before I do anything, but I've considered paint matched, since everyone is right, a black liner is always dirty, unless it's brand new. Even my new GMC, which came with one from the factory, and now has a tonneau cover, is still filthy. Not sure if a body colored liner would be any different, just that it wouldn't look as dirty as quickly... Just like your current color vs a black truck.
Oh, and the color fading, like Scoti said... a non-color matched liner would look funny regardless of the color (light blue instead of medium blue?). But, pink would be awful...