One of the first threads I started here was
WI Charles V divides his possessions differently? (https://www.alternatehistory.com/discussion/showthread.php?t=152714 )
First of all Charles V was born and raised in the Burgundian Netherlands, whereas Ferdinand was born and raised in Spain, for Charles 'Burgundy' was his heritage. OTOH Charles knew about the differences between the Burgundian Netherlands and Spain, when he became king of Castille (and later Aragon) he was seen as Burgundian, but in contrast his son was seen as Spanish in the Burgundian Netherlands.
Secondly Charles and Ferdinand were very loyal towards eachother in the beginning of their reigns, when their children became older, they became increasingly concerned with the position of their own house. Decreasing his son's inheritance, especially not giving him the lands he considered as a kind of home, in favor of his brother is a bit hard. If Charles V would have had a second son this would have been easier.
The option I mentioned in my thread was the (OTL) marriage between the son of Ferdinand, Maximilian II, with the daughter of Charles V, Mary of Spain, which could pass the Burgundian inheritance to them and their male line descendants.
Although I too suspect that the Austrian Habsburgs could have handled the situation in the Burgundian Netherlands better, maybe even because they were weaker than the Spanish branch. Which could allow for more political concessions, IOTL the conflict ('80 years war') had a political and religious component; removing most of the political concerns would win them the moderate support in the early stages of the conflict. That is if there is a conflict, it took some years to turn into a full conflict; Phillip II became sovereign lord of the Netherlands in 1556, but the conflict only really erupted in 1568 and was initially just against the bad advisors of their sovereign lord.
Regarding adding these lands to the lands of the Austrian Habsburgs this could improve the position of the emperor, although OTOH this will add an earlier French threat to the internal imperial problems and the Ottomans.