There seem to be two rather different things occurring here.
Generally, working on projects involving old films, there are reconstructions, and there are restorations. Occasionally, the two are performed concurrently, toward a final result that we attempt to make as transparent as possible.
Working in black & white, one has a bit more ease in massaging pieces together, but dealing with both color, as well as contrast and densities, can seal a work's fate, as some things cannot be put back together. Bits and pieces bump into one another.
In this situation, it sounds as if Mr. Leone's opus has been reconstructed, but not restored -- a hugely overused word, mostly for marketing purposes. If that is the case, and this is a reconstruction, it should be noted as such. Reconstructions are honorable works. Best to have probably begun with WB's HD master, and added the bits and pieces as they were, possibly faded and worn. The additions would then be obvious, and the point of the effort made. Quality footage is best not degraded.
In certain cases, where the necessary points of quality cannot be attained, some projects are best released on video, and not for theatrical dissemination.
This sounds like an interesting project, but if I'm understanding the background properly, might best have been reconstructed, with no intent of restorative efforts. Sometimes things are best left as found. As someone with great respect for the film, I look forward to seeing a reconstruction, but not a restoration.