But WI the proportion had been the opposite, and the couple had 04 boys (let's call them Charles, Ferdinand, Maximilian and Philip) and two girls (Eleanor and Isabella). How would the Habsburg territories have been divided between four heirs? Could we see an independent branch in Netherlands?
So would Charles still be the oldest?
Anyway, the oldest would inherit the whole thing, the entire 'Universal Empire'. How his brothers ended up would be interesting. The Kingdom of Spain, the Holy Roman Empire, and the Kingdom of Naples are all possible seats for different brothers. Add in a possible steal of Bohemia-Hungary or a grab of the Polish throne, all of which had electoral monarchies, so that those could be a fourth kingdom.
Spain as the jewel of the Hapsburg crown was mainly due to its American wealth and pre-existing connections to Italy. Spain was the logical crown to do most of the heavy lifting for the Hapsburg empire. Therefore it would stay in the eldest brother's line. I have always felt that the Burgundian Inheritance should go on its own, so there is another possibility. The problem with spinning the Burgundian Inheritance off is that the line who inherits that seat will become a competitor to the Austrian line for the Holy Roman Emperors' election.
I think that at least one and probably two of the brothers will end up without hereditary title. The brother who ends up the governor of the Burgundian Inheritance stands an excellent chance of being the Hapsburg who finally jumps and becomes an open Lutheran. Perhaps a younger brother?
A younger brother who is the governor of the Burgundian Inheritance and a Lutheran is logical- it makes sense in terms of politics. The French want the Burgundian Inheritance, but it would make more trouble for the Hapsburg to support a heretical brother than it would to invade that territory and keep the Hapsburg unified.
With the rapid spread of Lutheranism I think you could see the idea of Luther as a Catholic reformer instead of a heretic take root. Especially if the Burgundian brother is a religious man who agrees with Luther and patronizes him before any anti-Hapsburg German princes.