Looks like rust to me. @ OP (can't figure out how to type your name) was there a plastic trim piece over those thresholds? If so I'd have it at with dremel, then prime and paint (with Toyota color-match pen). Since its covered doesn't need to be seamless, just thorough.
May you provide a link to the item i can use to seal it and stop the rust? maybe some white pain to match it, i have never done this before and have no idea of what to use.
I've used Rust Mort, an acidic liquid. You brush off loose rust, then apply. It supposedly converts the rust to something stable.
