I'm pretty sure (although I haven't checked) that all the flags are national i.e. of a nation state. Neither Scotland, England, Wales or Northern Ireland are countries, even though they are referred to as such all the time.
It simply would not make sense, and indeed may cause unnecessary political bullshìt, to represent all possible regional flags (e.g. Cornwall, Basque, Quebec, etc.). National flags on their own can cause enough problems anyway in many cases.
Personally I barely consider myself British, let alone English (having been born in and raised in England) and the invisible lines only seen on maps don't seem to help the human race very much. I find the flags jingoistic but I understand why they exist in terms of FD revenue and I'm certainly not going to demand their removal. I still don't like them though and won't be buying any of them.