It hasn't been made clear how this started, I'm guessing that it was raised by a member of the public going to either their councillor or directly to the local authority. However, I can't see that the "upon direction from the Welsh government" phrase can be interpreted in any way other than the local authority sought guidance from the Welsh government and were told by them that the regulations did apply to Chester FC, as you agree above they do apply. If they were given that advice, Flintshire are hardly going to ignore it!
Both the County Council and the Welsh Assembly are Labour controlled, so I'm puzzled why you seem to want to put all the responsibility onto Flintshire rather than the Senedd, which doesn't seem entirely consistent with what Chester FC have been told. Have you other dealings with the county council, which has led you to this viewpoint?