My new 69 RR project now has black carpet in it, installed new by the previous owner. It's a 2 tone blue interior car. Should it have dark blue carpet or is the present black correct? I've had 69 2 tone green interior Roadrunners and their carpet was dark green. My initial assumption was dark blue for this car.

All 4 speed runners came with black carpet in 69

even ones with bucket seats & consoles??

"ALL" is rarely the case with anything

..... but I would assume that a bench seat M2B bench seat 4-speed Road Runner had "BLACK" carpet.

Read the notes

and if you read that chart, what color is the carpet in a '69 Road Runner automatic with the RM21 coupe's STANDARD M2B, M2T, M2X interior?

data & trim guides are exactly that "GUIDES" not perfect restoration reference "BIBLES"

Base interior column auto RRs got a rubber mat, according to both that guide and one of my original cars. That rubber mat was flecked with a matching secondary color (blue, tan or black). Decor automatics got color-matched carpet. My 4-speed RRs all had black carpet whether base or Decor interior. All were dead-original cars. Only combo I never owned was 4-speed w/buckets & console.
Could someone on an assembly line erroneously installed colored carpet on a car? Probably. I'd think in that case the car that was supposed to get that colored carpet would get black, and maybe that would go through or be pulled aside for correction.
Bibles, no, but an ordering/specification/production guide, yes. Picture the panic & problems if/when cars were assembled without specs being adhered to.

Talked to the previous owner and this M2B trim code car had black carpet originally.

I also had an untouched 69.5 car with two tone green interior back in 2000 and it had green carpet with the decor bench interior. I bought this from the original owner and the interior hadn't been redone yet.

Was it a 4-speed or auto?

4 speed car.

I know of a 69 GTX convertible that has a blue interior and is a 4 spd. I believe that Bill Allphin also knows this car as he owned it at one point and it originally had a blue carpet.

Console cars will have color matching carpets. Bench seat column auto cars will have color matching carpets. I had a B5 Hemi 4 speed Road Runner with B7 bright blue bucket seats non-console, blue dash, blue headliner, blue upper doors and black carpet. I have known a couple of 4 speed bench seat cars whose owner’s swore they came with color matching carpet but they were not the original owner’s and there was no real proof that it was original to the cars. Never say never but I Perdonaly have not seen a survivor to document an exception and I have seen a lot of 69 Road Runners.

Wonder why Ma Mopar would put black carpet in an all blue interior car, 4 speed or not? Especially when blue carpet was going in allot of other cars. That's why my first reaction to this was "this has to be wrong".

4-speed carpet is unique because of the 4-speed hump, so it would be simpler to make all 4-speed carpets the same color. Bean counters rule!

Exactly. There are numerous examples of Chrysler cutting costs pretty much every time they found an opportunity.

the Road Runner was originally based on the "cheap seat" Belvedere 2 door sedan (post coupe)
the M2B, M2T, M2X Belvederes have rubber floor covering STANDARD
there is NO rubber floor covering available for the STANDARD floor shift 4-speed Road Runner
so "BLACK" carpeting was substituted

at some point in its development Road Runner received carpeting STANDARD

the dealership's guides contradict themselves, just a by-product of trying to keep up with running changes

the assembly lines would have their own build procedures & would not have dealership trim guides as instructions to assemble cars

I don't think it was a cost cutting/saving measure

the same scenario happened with the introduction of the '69 340 Swinger on the a-body line - cheap interior with rubber floor covering - 4-speeds got black carpeting

due to the popularity of the cheap go fast a-bodies - 4-speed rubber floor covering showed up for '70

never seen a colored interior '69 4-speed B-body w/console & original black carpet
never seen a colored interior '69 4-speed Charger/Super Bee or R/T w/original black carpet

never seen a colored interior '69 4-speed A-body w/console & original black carpet
never seen a colored interior '69 4-speed Barracuda/GTS w/original black carpet

also, I've never seen a '69 RR with rubber floor covering

A guy would have been good with black carpet. Perhaps only the cars that women drove had colored carpet!
My 4-speed coupe is black.

My original 69 Formula S console 4 speed car has yellow interior and black carpet.

The yellow D6P interior would be the exception to the rule. A yellow carpet would be a little too much...