Remember: This is an Opinion.
I don't see why one little flag should matter.
I don't think they're paying tribute to the country, i think it's NT's personal mark. "We are an english/british developer, therefore we'll put something on it that represents us"
In fact, I've been meaning to post this:
I was playing Blood Omen 2 a few weeks ago when I found this in one of the chapters (chapter 4 i think)
If you notice the shield on the stained glass window, you will notice a red and white cross.
The red cross and white background is the english flag (just in case you don't know), does it have any influnce on where the games is based? Does it make Kain English/British? No.
If Dante is a Punk. It's more than likely to be a 'sewn on' patch.
I think that with this reboot, there are other things to worry about than a little flag.