The viewfinder screen needs to be in the exact, right location to determine focus. if the viewfinder screen needs a spacer underneath it (as in the form of, say a foam square, or a leather square, or a metal spacer) to equal the flange-to-film distance, then the viewfinder image will show **the wrong focus**.
If the flange-to-film distance is not exactly proper, to within a few thousands of an inch, then the focus will be way off at Infinity. This is what spacers are so,so commonly used inside the lens mount area, on hundreds and hundreds of film camera models: shimming the lens mount to the exact, correct distance is very commonly used as the way to regulate lens focus.
As to "blaming the lens"...it could be a lens issue, but it is more likely to be the viewfinder screen, or the lens mount and the flange-to-film distance--but who really knows? Does the issue persist with another lens? Does the problem persist with a different film back? You have not described in much detail the flaws, nor what cross-checks you've performed, so this is mostly speculative comments on what "might be" the problem(s) you're having.
I tend to agree with you that the lens is not to blame here...my money goes on a MIS-aligned viewfinder screen, or a MIS-aligned (out of specification) lens mounting flange that is not at the right distance. But again--not much information here, on a complex mechanical system.
But let's go back to the scenario you listed: " if an object is 10 ft away, even if the distance scale on the barrel reads 12 ft, but the image in the viewfinder is in focus, shouldn't the image on the film plane be in focus too? If not, that seems like a body problem, not a lens problem. What am I missing?"
Body problem: viewfinder screen is not at the right distance Lens mount is not at the right distance. 10 feet and 12 feet are NOT close enough to cover the depth of field. Lens mount, camera mount, viewfinder screen, film plane alignment: could be a problem anywhere in here.
Lens problem: who knows who has worked on the lens, or repaired the lens, our disassembled and reassembled the lens, over the past 24 years. it **is** possible that the lens could be improperly re-assembled. I am not a repairman, but...if the lens mount is not 100% at the right distance to the film....that could explain the problem of a 10 foot and a 12 foot discrepancy causing the problem. You have a pieced-together outfit made over decades...what about the old film back, made in 1975? That too could easily be out of specification. You have lens mount; flange-to-film, viewfinder, body of camera, and film back and film plane issues to worry about. Six areas. Six.