Mary's Habsburg marriage and birth of heir will cause panic in France. Next Habsburg-Valois war is guaranted. With Philip being more than occasional guest in England English entry to the war from very start is likely and English actions would be better coordinated with Imperial ones. Also Habsburgs are not going to give up Calais if it is part of future inheritance of Habsburg prince. So France is likely more beaten than after OTL 1551-1558 war and has worse perspectives for the future with Habsburg encirclement from every side.
So if Mary of Scots is not in France and didn't married Dauphin yet, would she? Now when France is in similar situation as in 1520s? Valois marriage of MQOS means Scotland is thrown by default into Habsburg-Valois conflict on the weaker side, so in the case of another war Scotland is thrown under the Anglo-Habsburg bus.
In the scenario you describe the Scots would be absolute fools to ally with the French, let alone marry their Queen to a Valois Prince. They've lost two Kings in less than thirty years due to the Auld Alliance and now their great enemy is directly married to the most powerful monarchy in Europe. No the Scottish Court's best bet
is to jettison the Auld Alliance and France completely. Now assuming this happens, the next move should be either a reconciliation with England or an alliance with Austria. If they go with England the likely candidate is Mary's OTL second husband, Henry, Lord Darnley. He's basically the closest thing England has to a Prince, being Mary I's only Paternal male relative, and due to his mother's close friendship with the Queen is the likely candidate. Plus he's half Scottish, his father being the 4th Earl of Lennox, so the Regents might be able to stomach it. Or, if not, then they should look to an Archduke, like OTL's Karl II of Inner Austria. A Habsburg consort would be a shield from English aggression, Mary being unlikely to wage war on her husband's brother-in-law (Karl's brother Maximilian was married to Felipe's sister Maria).
The marriage contract was that the Netherlandish inheritance would pass to the kids of Felipe and Mary (as a secondary split from the Habsburg inheritance), in addition to their English inheritance from their mom. That said, the marriage contract also (AFAIK) prohibited a union between England and Spain - i.e. if they'd only had one kid and D. Carlos died without issue, Felipe would need to remarry again, since England was fearful of becoming yet another appendage dangling from Spain's belt like Naples or Burgundy. Which is why I asked, in
@Kynan's posited tree, with two sons, should D. Carlos die on schedule as scheduled (questionable here, since IDK if Felipe II would necessarily snake Élisabeth de Valois or Anna of Austria from him), would the duke of York succeed to the Spanish throne. Or would Felipe be required to marry again after Mary dies in order to shore up the Spanish succession.
Not true. In my biography of Mary I,
The First Queen of England: The Myth of "Blood Mary" by Linda Porter, such a caveat is nowhere mentioned. In fact, it's stated that "In Spain and Italy, Don Carlos would become ruler, but if he died without children, any male heir of Mary and Philip would succeed in those lands as well as the emperor's in Burgundy and the Low Countries. If there was only a daughter of the marriage, she would rule both England and the Low Countries, but not elsewhere." Clearly Mary and Philip's male heirs had full rights to Spain and the Italian states. So if Carlos died childless his next brother would succeed him, either as Sovereign or heir, irregardless of him being King of England. In fact this is specifically spelled out in the actual Act of Parliament that dealt with Mary's marriage,
Act for the Marriage of Queen Mary to Philip of Spain. Here's the relevant quote (I can link the entire act if you with) "....but if it fortune the same lord Charles to die, and the issue of his body to fail, then and in that case the eldest son of this matrimony shall be admitted into the said right, and according to the nature, laws and customs of the said realms and dominions shall succeed: the same eldest son shall also succeed in all the dukedoms, earldoms, dominions and patrimonial lands belonging unto the said lord the emperor, as well in Burgundy as in the lower Germany;...." That's the official Act of Parliament; if any ban on a personal union was included in the marriage treaty it would be in the Act.
Of course, with a 1546 POD it's by no means guaranteed that Carlos would die childless, though considering his delicate health, extreme cruelty, and mental disabilities (the first two where definitely before his 1562 fall down the stairs but am unsure if the last was caused by the fall or if it mere exasperated the preexisting issues) it's still quite likely. Now I could be wrong and Carlos could surprise us, assuming that the mental issues were caused by the fall. His health was delicate but it didn't get bad until a bout of Malaria at age 11, so that's easily butterflies here. He was extremely cruel and sadistic but so was the highly successful Ivan the Terrible. Finally, in OTL, his would-be wife and eventual Step-mother Elisabeth de Valois seemed to exercise a moderating influence over the troubled Infante, so she might be able to do so TTL, perhaps to a larger degree.
Something else to consider is just when Carlos dies (again assuming childless here).If it's before his stepmother, then there is the possibility that Mary and Felipe could play some musical thrones and make their eldest son heir to Spain and Italy and leave a second son to inherit England, Ireland and the Low Countries. However, if Mary is dead and her son is King, then I don't see him renouncing his rights to Spain and the Italian states. After all, there's no precedence in favor of such a decision and in fact Habsburg precedent would favor adding England and Ireland to the Spanish patrimony. So there would be the risk of a succession crisis or war if at Felipe II's death if he tried to forcefully disinherit his son the King of England.
Finally and this is just a thought, but I wonder if we could see a triple division of the Habsburg realms at Charles V's TTL abdication. OTL he gave everything to Felipe over two years but if he had an English grandson destined by treaty to inherit the Low Countries, then there's the possibility that he could go ahead and pass the Netherlands to the Prince of Wales. Not likely but just a thought.
