This doesn't sound like a rangefinder issue to me as I'm not using the rangefinder, just focusing on a ground glass.
First, if you just bought it, and it's returnable, then that's probably the fiscally most sound decision.

A problem like this can eat up a ton of your time and still be uneconomical to solve. That said:
You're right that it's not your rangefinder, and it's pretty unlikely that there's anything wrong with the camera body. In order for the camera body to be the issue, the flange black, a.k.a. flange focal distance (i.e. the distance from the lens flange to the film plane), would have to be incorrect. That is possible, but not terribly likely, IMO. You could check this by researching the flange focal distance for the Mamiya Press cameras, then measuring yours, but you'd need good calipers, I think, in order to get useful information. I loosely measured the flange distance on my Mamiya Press Universal once at 53mm, but I did not use calipers, so don't take that as the correct figure.
So that leaves the lens. There is no user adjustment for this, but it is entirely possible for the lens to become misadjusted in this way with improper repair or mistreatment. Depending on how the misadjustment happened, it might be relatively easy to fix. I've partially disassembled two Mamiya Press lenses; one (the 150mm) was fairly easy to get completely apart, including individual lens elements, and the other (the 50mm) was not. I was able to put together a quite sharp 150mm lens with an accurate shutter out of two junkers (for a total of $30). My 50mm, however, is defying me at every turn, and I'll probably have to bite the bullet and pay a professional to fix it.
I'm guessing you have a 100mm (i.e. normal) lens? I haven't tried to dig into that one, so have no idea how easy or hard it would be to check if the focus barrel/helicoid is assembled correctly, or whether a lens element is installed backwards (not uncommon) or something like that. If there's a repair shop near you, it's probably worth asking them. But it's very likely that it would be cheaper to just buy another lens. Again, that makes sense only if you can't return the camera for a refund.