People need to look at history, the only English King Regent was William III and he only got it by blackmailing Parliament ( pass a bill declaring I'm co-monarch with my wife or I will not help you depose James II ). Therefore James is getting King Consort at best , the rule of what is the wife's is the husbands only apply to non titled folk. Entailed lands and titles might go straight to a son but never a husband without an act of Parliament.
Parliament at the time of William and Mary held more power than it did in the 16th century. Royal power had eroded somewhat by that time. James will be King. (I'm not sure the term "King Consort" even existed or would make sense to MEN in the 16th century. Ferdinand wasn't called King Consort, he was called King even though his powers in Castille were limited by a treaty). James has custody of Margaret's heir apparent (Arthur) and he can/will blackmail her into proclaiming him King of England. All he has to do is stay in Scotland. It's not like she can go get pregnant by, say, Thomas Boleyn and declare that bastard King. She needs James more than James needs her. She needs his experience, she needs him to father more children by her, etc. Parliament can try and get James to agree to a limitation, but it's really going to fall to Margaret to want that before it happens. She was ruled more by her heart than her brains (unlike OTL niece Elizabeth), so it's probably going to be James King of both countries because of this. She was in love with the guy.
Also, the crown is not subject to the rules of the nobility (re: entailed lands and titles). And Charles Brandon got to be Lord Lisle on the basis of a betrothal without an act of Parliament, so that rule you're citing is flexible.