It's a topic that's been thrashed out a few times here, and there are exceptions to the rule for the highest trim levels, and for a couple of cars, apparently what was available when the car went down the line.
I can't speak for A & E bodies, but all of my original '68-'69 Road Runner 4-speed cars had black carpet regardless of interior color; but they were all bench seat cars with either standard (Belvedere) or Decor (Satellite) interiors. My base model '68 A/T RR had the rubber mat, and my Decor '68 had color-matched (burgundy) carpet. Dodge may have had a different scheme, but my only 4-speed Charger had white/black interior, so its black carpet is no help to the topic.