I thought so, too, Yardstick, based on what I'd "heard." But then I started my research into the question, and quickly realized that there was simply no way that Charles Thomson would have used Masonic symbols!
Check out his biography at the link provided at the top of the article, and see whether you agree.
In 1782, no more than four people were involved in the development of the Great Seal, and not one of them was a Mason.
Thank you again so very much for this wonderful essay!