is there a way to have Trading Networks set the remote file name of documents it delivers via FTP?
If you are going between internal IS server, there is no need to do that, using deliver as Primary FTP alleviates that requirement.
However, if you are delivering to another partner for example, then what was done here is to write an FTP delivery service which draws FTP override values from extended fields in the partner profile. This would also work going to any system internal or external. Our company has been using a FTP delivery service we wrote to ftp flat files from our IS servers to AS/400s.