The OP wrote the title of the thread incorrectly as Northampton Town NFA side are the county side not NTFC.
Where are you getting that from?
1/ Why would the NFA let the county representative team enter the county cup and what would be the point?
2/ 3 players from AFC R&D are in the county side and none of them are anything to do with NTFC.
3/ I have heard a direct quote from someone within the NTFC youth set up saying that it is the official youth team as 'there is no-one else'.
4/ It is on the official NTFC website that the youth team are playing AFC R&D.
So I don't know where you are getting your information from but to my knowledge you are incorrect. If I am wrong, then I apologise... but I'm pretty sure that I'm not.