That doesn't seem like too much of a mystery. Sure we don't know how he did it, but there are other techniques like it. For instance, Oro "reviving" the dead. More specifically, restoring their personalities to their bodies. While their "spirits" might not have existed on "earth", we can guess that wherever they existed, was accessible to humans with enough knowledge about that kind of stuff. You would imagine a similar principle for summoning the death god. He might not exist on earth, but wherever he does exist, someone with the proper knowledge can gain access to him. I mean, I may have written the obvious, but that's kind of what the question called for, because we all know that there are things yet to be revealed in the series. The rules have not all been laid out, so to speak.

More specifically, there probably is a spirit realm in the narutoverse. Kishimoto did say in an interview that Narutoverse "jutsu" are nothing more than D&D type spells with somatic components replacing verbal components. D&D had spells of that nature. So, it's reasonable to assume that there's some kind of incantation (instead of jutsu, because of the nature of the subject matter we're discussing) that allows access to the spirit realm and communion with it's denizens. Furthermore, we all know Kishi is a big dragonball fan, and many of the things in Naruto are in homage to that series and its sequels. Dragonball as well as dragonball Z had such a spirit realm. Hell, the living could travel to and from it and remain alive.

So yeah, Minato encountering a death god doesn't seem that big of a mystery, there is precedence for it happening, and several reasonable theories as to how it could happen.