I’m not sure that it has to be purchased separately as every installation that I worked on had it.
As for upgrading, yes! Do it if you can as 6.01 has many improvements for handling flat files. As wm now distinguishes flat files from EDI files. These improvements includes things like the schema editor for building the structures, this replaces the templates I mentioned earlier. Also the capability to extract info from the flat file doc types definition, something that was reserved previously for XML doc type definitions.
That being said 4.6 can and does handle flat files.
m2c
#Integration-Server-and-ESB#webMethods#edi