Actually, there were: between 1725 and 1825 most of the Russian rulers had been either installed or deposed by the military coups. But you are seemingly missing a fundamental point because comparison is not with Mary. Both Peter and Catherine had been brought up and operating within exactly the same political framework and Peter ended up being overthrown by Catherine because she was intelligent enough to adjust to the system while he was expecting that the system will adjust to him just because he was a legal ruler. That's how you can distinguish the smart person from not too smart. The same goes for the systems with the parliamentary "checks": Gustav IV of Sweden had been forced to abdicate and go to the exile while Jean Baptist Bernadotte (who was a complete stranger to the system) founded a dynasty which still reigns in Sweden.
The rest are just excuses.
Sorry, but you really don't know subject well enough. After his death Catherine did not repudiate the peace and was quite cozy with Old Fritz and nobody blamed her for that. Peter's fatal mistake in this context was a declared intention to send the Guards to participate in a planned war against Denmark: the Guards had been quite happy in St-Petersburg and had not intention to go to any war. Conflict itself was, for Russia, a typical "cabinet war" and Russian nobility was not excessively happy paying for it (and nobody really needed Eastern Prussia, anyway) plus, by the time of Peter's accession, Russian-Austrian relations had been already fundamentally spoiled making further fighting rather absurd.
I'm well aware Catherine did not go to war, but you are one making the comparisons of Mary and Peter. So, you have to excuse me if I'm not too knowledgeable, and I feel the comparison of their situations or even grouping them is not at all justified.
The military does not count as a formal check on power that a parliament or another legislative body is. If we are going by that logic then the Roman Empire, Ottoman Empire, and Ming Dynasty were basically not autocracies because rulers could not use their full by powers by the "check" of factions either willing to play kingmaker, if they do not get their way, or obstruct government by corruption. Russia was still an autocracy with no formal checks, Peter could do what he wished with his right to govern, Mary knew she was limited by parliament and did not stir the pot too much, it is not like she was her was grandson Charles.
Mary's fall was not due to a foolish attempt to flaunt her own power in the face of everyone else, or by angering the wrong people especially since she started to dislike Lord Darnely as well, but a conspiracy made behind her back, with the possibility of the conspirators being bribed or threatened. A conspiracy she could not predict nor realize it would go south the way it did, even then that fall, boiled down to one battle.
Her marriage having unforeseen consequences is in no way similar to ending a long war on a white peace or trying to expand in relatively distant Denmark. What I'm trying to argue, and I do not know if is getting lost in all of this, is that Mary could at least be a moderating influence with a surviving Francis II. Her fall in Scotland was both unpredictable and irrelevant to this question since Mary won't have to worry about marriage again, more so if she has a son with Francis, which means a completely different situation for her. She knows she cannot do much in Scotland that could upset the religious balance, and she basically did not do so for most of OTL. She is his wife and could have a role unless you think she is bad at that too. If a union between France, Scotland, and possibly later down England is ever going to have a shot at working, Francis II would have to realize that a comprise would have to be made especially since Scotland helping Scotland relies on England not getting involved, which would make his marriage to Mary pointless.
How exactly would it butterfly the Vassy other than in not having any accommodation in the 1st place? The Guises are still in power and the Protestants are still mobilizing for fight. As for St. Batholomew, please explain how events which lead to it would be substantially different, why would he find himself in a stronger position than Charles IX, why would he be more tolerant to the Huguenots and why Huguenots and Catholis would hate each other less than in OTL?
The Events of St Bartholomew came about from the marriage of Henry III of Navarre and by extension the peace of the third war of religion in France, the first of which started in 1562. Vassy itself happened because of an apparent lag in the implementation of the edict of January, Vassy happened in March. It could be possible for an earlier edict, depending on how one wants to play with butterflies, and I believe those specific events can be avoided, not that a working religious peace can be made in a short amount of time, but that a slightly less bloody situation can be made out of it.
Spanish Florida could be butterflied away or delayed, so that a Protestant colony can be formed allowing Protestants to head to an ATL Florida, as an opportunity to release tensions. There are still plenty of events that could negatively impact Spain, to benefit France's domestic situation with religion. As for why he would be different from Charles IX, I do not see why he or his situation with Spain would be the same, you could have Philip II's unstable son in the Netherlands instead of the Duke of Alba, considering butterflies can allow it. The Ottoman siege of Malta could still be up in the air but Francis surviving be would after the Ottoman victory at Djerba. The Ottomans are still a threat to the Hapsburgs as a whole period.
Don't mind my insistence on pursuing this topic, It is giving me some ideas on what to do with Western Europe for my own timeline. Granted my timeline's POD, with a more self-contained POD, is earlier than Francis's death, and believe that anything goes after the fact at least event wise.