I'm still somewhat of the opinion that once Spain and France are both in the war, the result will be that they concentrate on each other, what with their land border and their need to compete for predominance in Europe. This will give the Dutch leaway to revolt, and since the English only need to defeat what comes across the sea - not easy, but as I alluded to before, with Spain actively attacking France and vice versa I don't see either of them managing to raise a 130-ship Armada any time soon. The English managed to mobilise 45 ships to fight the Armada and the Dutch sent another 80, and even though these were small galleases rather than the galleons the Spanish had, all they need to do is delay their attackers until they hit the North Sea, where the tides make it harder to return back onto a course for England, and they'll either drift towards Scandinavia before they can get back to land and return home, or they'll be caught in the round-Britain currents as the 1588 Armada was. That's not to say that the English will definitely win, and will avoid being invaded, but their cause isn't hopeless by any means.
Really I think this conflict is too complicated to predict, so if you want to write a TL about this scenario, it's entirely down to you to write the events.
Incidentally, while the Scottish commons weren't so pro-active as their English counterparts, the Scottish nobility was becoming more Protestant in this era. It was for this reason, after all, that the Catholic MQoS was driven out of her country and into England.