My interpretation of what OP is asking is "why does JDE have 2 differently referenced systems that bring in outside data?" Why is AP and AR typically brought in via Z-file processes, but sales orders, invoicing, ASN's and others have something called a system 47?
I've worked extensively with both over the past 17 years, and I don't think there's a good answer as to why JDE decided "this one is 47, but this one is Z-files". If I had to guess, I'd say that they tried to marry the typical ANSI-X12 standard EDI docs that manufacturers typically exchange (850, 810, 856) to something with an overarching name called system 47. I think system 47 processes are a bit more robust/complicated. More screens and logic dedicated to them. Whereas the Z-files, though effective, are a little more "thrifty", if you would. The initial interfaces are maybe a bit more basic, the UBE's that process them aren't really more than shells which call the same business functions that are used in the interactive screens to process data. System 47 re-uses some BF's too, but again in my experience they're a bit more robust.
The bottom line answer is they both serve to process in outside data (or prep internal data for transfer), but just have different system codes.
Just my opinion on this, others may disagree.