Well the inheritance wasn't split at one point. Ferdinand got the Austrian Hereditary Lands including the share Charles V was entitled to in 1521, though arguably between 1519-1521 there was at least nominally joint-rule in the Austrian Hereditary Lands, which unlike Castille, Aragon & 'Burgundy' followed that 'German' tradition. However at the same time Ferdinand initially wanted more, which probably means the Burgundian Inheritance and the Habsburg Candidacy for the Imperial Throne, since Charles V had already succeeded to thrones of the Crowns of Castille and Aragon in 1516. The duchy of Milan wasn't on the table yet. Still Ferdinand getting the entire Austrian inheritance was already a sort of concession from Charles' point of view, it was a practical one, since it made governing easier and it strengthened the position of Ferdinand as an ally for his brother in law Louis II, king of Bohemia and Hungary, against the common Ottoman threat.
Charles V invested his son Philip as duke of Milan in 1540, so before Charles V abdicated in 1555.
By the point of the abdication of Charles V the only things on the table were Castille & Aragon, and the Burgundian Inheritance. There's no doubt his son would get Castille & Aragon, so this leaves the Burgundian Inheritance. Charles V would be adamant about the fact, that Burgundy stays in the family, so it would pass to his daughter Mary and her husband, his nephew Maximilian II, under the condition, that if Mary were to die childless, the Burgundian would revert to Philip II. The downside of the Burgundian Inheritance is a more direct threat from potential French expansionism, however it does add a large source of income, if managed well, and who knows future colonial endeavours, but let's not get ahead of ourselves.
Moreover again I can't see Charles V stripping Philip II from Milan, if Philip II already loses the Burgundian Inheritance, also technically Philip II would need to give up Milan, which IMHO is unlikely too. However IOTL Philip II did give the Spanish Netherlands to his daughter Isabella and her husband Albrecht (a son of Maximilian II and Mary), which would have become hereditary for their line, if the had surviving male children, ITTL Milan would be a good territory for this.
Alternatively Milan might at one point shift to the Austrian branch as a dowry, when a Habsburg Spanish Infanta, marries the oldest, and thus main heir, Habsburg Austrian Archduke. It's a big if, but it might be that the ruler of Spain finds, it's not worth the trouble any more, whereas the Austrian branch would definitely be interested in Milan. I just can't see the Austrian Habsburgs gaining the Burgundian Lands and Milan in 1555; now if Ferdinand for some reason inherits the Austrian Hereditary Lands & the Burgundian Lands in 1519/1521, and he becomes Elected Holy Roman Emperor in 1519, then I can see Milan ending up with his branch, since it is an Imperial Fief, though to capture it Spanish help would be needed, so it would pass to TTL Maximilian II & Mary. Actually Ferdinand being elected Emperor in 1519 instead of Charles, might help to establish a Castille-Aragon and Austria-Burgundy division.