I understand what you're saying but to think of this as the rangefinder of a $3000 camera would be a little misleading. The R-D1 is based on the CV Bessa R3A, which is a $540 camera. The Bessa is designed for value and it is significantly less expensive than the other aperture priority options (Ikon at $1400 and M7 at $3500). Why did Epson go with Cosina? I suspect that it was the only option they had. No one in the world other than Cosina (to my knowledge) sources rangefinders, bodies, etc. for other manufacturers. It's no coincidence that the new Zeiss is also Cosina-based. Leica seems to be the only other major company in the world right now with the tooling and knowledge to make RF cameras. Others, such as Canon, could potentially do it from scratch if they wanted to but I've seen no evidence that they have any interest. If Epson hadn't been able to get much of this camera from Cosina, there would have been no R-D1. So the R-D1 has the RF of a $500 camera that was designed and built for value.
What made the R-D1 so expensive was the R&D time and investment that was needed to turn an R3A into the world's first digital rangefinder. All that investment, moreover, has to be recouped from the sale of just 10,000 units. The chronograph style displays all by themselves were likely pretty pricey to create and manufacture.
One could argue that perhaps Epson could have planned on 30,000 units selling for $1500 each (I'm just giving hypothetical numbers here, they're not from my sources at Epson). Maybe that would have worked financially and maybe not. At 10,000 units however, if the R-D1 had been based on a $1500 film camera, it likely would have cost $4000 instead of $3K.
The following is not official but my conjecture is as follows: Cosina manufactures their part of the camera and sends it to Epson with the rangefinder (supposedly) adjusted. We know that some Bessa film cameras come through with misadjusted RFs but it doesn't seem to be that many. Epson then needs to complete the manufacture and I suspect the body is subject to various forces during those parts of the assembly process. I wouldn't be surprised if many cameras go a bit out of RF adjustment during the "digital" part of the manufacturing process. I'll also bet that the cameras don't go back to Cosina before being shipped to dealers, etc. Ergo, unless the Epson factory has a facility to automatically check and adjust RF adjustment after assembly and before shipping (and I'll bet they aren't set up to do that), the units go out as is with the (perhaps faulty) assumption that they are adjusted as well as they were when they left Cosina.
Epson really needed to stretch themselves a bit to build this camera. It required tooling and facilities they don't have and, frankly, some expertise that had to come from Cosina. Leica, by contrast, has the knowledge and facilities to make sure that every digital M camera that goes out has a properly adjusted rangefinder. The Leica is also based on a much more expensive camera (the M7) and so the rangefinder components themselves are of higher quality. And...Leica has a dealer and repair network that knows M rangefinders.
So, if one looks at the whole picture with the R-D1, it's rather amazing that it actually came to be produced at all and (while it's dissapointing), it's not entirely surprising to me that the rangefinders on these cameras are often out of adjustment a bit when they arrive in stores. That's not to excuse Epson but I still am grateful that they produced the camera at all, even with the problems. They were daring and not everything has gone smoothly but at least they actually did it rather than playing it safe and not making production cameras.
I do wish, however, that Epson USA had taken my advice and set up with Stephen Gandy, Don Goldberg, etc. so that cameras that needed RF adjustment could be dealt with properly under warranty. I can't image that orchestrating such an arrangement would be very difficult compared to the challenges of making the camera in the first place. It should have happened. They expressed a lot of interest in the idea but they ultimately didn't do it.
Cheers,
Sean