Was Jane Queen?
You keep asking this and you keep getting answered. Yes, England is never without a monarch and she was it for those few days. If the current Royal Family say that she was Queen, will that satisfy you?

I believe the way it works; The Lord of Lyons is involved in determining the Chief of a Clan. Particularily where there are issues - such as the Gray-Campbell issue in the 1950's. The chief of the clan, then is entitled to make the decisions for the clan - such as matters concerning the tartan.
The problem is that your belief is misguided. The Court of the Lord Lyon only covers Heraldic issues and only applies to those clans it recognizes. It only applies to the commercial use of the clan name when that clan is covered by the Lyon's Court. It doesn't apply to the general public wearing of the tartan. It doesn't apply to those clans not under its ruling. And it only refers to the bloodline aspect of the clan structure, which is only one of the three parts of the clan structure.

What is happening here is that there is a legal definition of clan that is necessary for heraldry, land, and identification. There is also a social definition of clan that applies to everything else and that's where who gets to wear what tartan comes in. You might want to look at clan in Wikipedia, it's a pretty good article.