There is a property on the flat file disassembler to put the data you define as the Header (in the header section of the disassembler) into the message context.
Don’t forget there is a 255 or 256 character limit and I think it’s just put the data in the header as flat file text (not XML). Not really sure though, I’ve never done it. It would mostly be used if you want the header in your output message.
Hope this helps.