I think Philip II match both of your points (in my opinion, of course);
1) He has been leader of both civs at the same time and in the same period of time (Both Spain and Portugal in Civ VI are from the same period).
Actaully, it doesn't match my point (but I think I wasn't clear enough on this one). For me, a good Cuv dual leader should have been the leader of the historical civ
at different times, to justify the fact that they can lead one or the other, but not both at the same time. That's for me the biggest counter-argument against Philip II as a leader for Portugal.
During the Union, Portugal was just another realm of the bunch that formed "Spain" (Castile+Portugal+Aragon+Navarre) nor more, nor less. And for me, Yes... I can imagine Philip II as a leader for Portugal as it was king of Portugal by inheritance.
For me, then, by this vision, Philip II is even less justified to lead Portugal. As you said, Portugal was
part of Spain, not
adjacent to Spain. Compare with Eleanor, the Ur-alternate leader: when she was queen of France, England wasn't
part of France, it was a different country.
- Philip became King of Portugal BECAUSE OF support within Portugal
From what I read, Philip II sent his troops
before the artistocracy elected him, and he was elected when he militarily won the war... The crisis succession of Portugal at this time is notoriously controversial (was it an invasion or not? Historians seems to still debate on it), so I'd prefer to be on the safe side and say that, in the case it was truly an invasion, Philip II as a dual leader is controversial.
What I feel the design of Firaxis was (explaining why they went with the quite obscure exemple of Eleanor first and not, say, William III of Oranje-Nassau for Netherlands and England, or Charles Quint for Germany and Spain) is that the two leaders
have to not be the leader of both civs at the same time. Both civs need to have been
different countries when those leaders were in charge. And I'm sorry if I'm a little old school, but for me two countries that share the same Head of State cannot be consider truly separated from one another.
Once again:
Philip II was mostly King of Spain. From his 28 years old until his death, he has been nothing but King of Spain(s). Having him represented without his main posession would be like if Victoria led Canada or India: sure they were their lands, as Queen of the Commonwealth and Empress of India, but nobody would ever doubt that Victoria without England (or at least Great Britain) is simply not Victoria.
The very identity of Philip II is Spain, starting when he was 16 as a regent for Spain (not Portugal). Portugal seems so anedcotical in his vast
spanish Empire that making him lead Portugal while wompletely erasing all of what made him him, seems counter-intuitive.