In B2B agreement, just "uncheck" translate checkbox and deploy, it will not convert to XML and you can get the same payload that is received from partner
Dude, I think you are talking about transforming without using a transform..I assume you are using a standard X12 850 or EDIFACT ORDERS File and wish to translate it to a Positional Flat file.
I do not know of any other method that using B2B adapters at either end and using their respective schemas and translating the output.
For a very high level approach , it would be something like this.
IN_B2B ==> BPEL(Recieve, XSLT, Invoke ) ==>Out_B2B
Let me know for further help.