Protestantism evolved differently in Scotland than in England during the 16th century reformation, with stronger Cavinistic influences, for example. Whereas in English protestantism, the monarch was, and is, the Supreme Governor (ie “head“) of the Church of England (and not subject to any other human authority, specifically the Pope) the tenets of the protestant church in Scotland state that “the Head of the Church is Jesus Christ”. Whereas a new British monarch automatically becomes Supreme Governor of the Church of England, he or she has no special status in the Church of Scotland and is simply a member of the church alongside all other believers. Part of the deal for the union of the parliaments of Scotland and England in 1707 was that this distinction would be preserved and that no British monarch would try to assume headship of the Church of Scotland. Every new British monarch since then has had to make that promise, as Charles did yesterday.
In constitutional terms, this acknowledges that while the Church of England is the established church (essentially the national church) of England, allowing blurring of church and state and the reason why some bishops sit in the parliament in the House of Lords, there is no established, national church in Scotland and a clearer separation of church and state.