@EMT: interesting analysis. IMHO in a scenario, where Charles V would transfer away his patrimony, the Burgundian Inheritance, from his son's inheritance, then if only as kind of compensation he would allow Philip II to keep the duchy of Milan. I know that the Austrian Habsburgs also had claims on Milan, given the strategic value, also to protect the Austrian Hereditary Lands. Still Milan in friendly Spanish hands is preferable over a French Milan.
Moreover Ferdinand, with more realistic religious policies than either Charles V or Philip II could continue to profit from the Netherlands like the 'native' Charles V, something the 'foreigner' Philip II never could. For starters he broke his promise to regularly visit the Burgundian Netherlands, he visited once and never returned, whereas Charles V was 'one of them'. Given the ability that the Spanish raised Ferdinand showed to integrate in his Austrian possessions and the Empire.
Still IMHO a better division between Castille & Aragon and Austria & Burgundy and the Empire, might be achieved easier when Philip the Handsome survives. Since otherwise, knowing Charles V, he might give the Burgundian Inheritance to his daughter Mary, married to the eldest son of Ferdinand, Maximilian (her cousin), than to give it directly to Ferdinand at that stage.
Another scenario could be one, where Maximilian I of Austria outlives Ferdinand of Aragon for a while. Then Ferdinand could be positioned as the Habsburg heir in the Empire. Charles will get Castille & Aragon, while Ferdinand will receive 'Burgundy' and later Austria.