As someone with strong Scottish ancestry, I respect the need for some to refer to James I and II as VI/VII since they were completely separate countries until the Act of Union.
There was a legitimate campaign back in 1952/3 for the new Queen not to be known as Elizabeth II in Scotland (even made itself into a song "She might be the Queen but ye cannae have the Second when the First one's ne'er been") Given that Elizabeth I did have a passive claim over the Scottish throne it was seen by some as a concession too far.
For the record, the relationship between Elizabeth and Mary Stewart was my own focus during my Honours History. I left with a far better impression of Elizabeth than I had of Mary