This is an interesting "what if" for the reasons stated. The Netherlands are within the Holy Roman Empire already, and the Austrian branch did tend to be more lenient to the Protestants, and more critically, less centralizing than Felipe II proved to be.
The big problem with this is that the vast bulk of the Carolingian inheritance did pass to the oldest son, Felipe II. Ferdinand got the following:
1) The imperial title. This was elective, and there was really no way to prevent this going to Ferdinand, who held the Bohemian crown and its electoral vote in his own right, and was preferred by the other Electors as the man-on-the-spot defending Germany against the Turks.
2.) The collection of territories that later became the modern states of Austria and Slovenia
3.) Bohemia and the crown of Hungary, these were both elective monarchies and Ferdinand had married into their royal houses.
Really only the Austrian/ Slovenian collection of territories was conceded by the Spanish branch to Ferdinand. His claim to Bohemia was by marriage, and the Electors would prefer a King of Bohemia to a King of Castille as Emperor.
Felipe's territories within the Empire consisted not just of the Netherlands but of Milan as well. Both were wealthy places and it would be a big concession to hand over both to Ferdinand. Plus Felipe had spent much of his life in the Netherlands and thought he understood the place well. And he was married to the Queen of England in the 1550s, which naturally goes better with the Netherlands inheritance.
It really would take a decision by Felipe himself that he had enough on his plate with Castille, Aragon, Sicily, and the Americas and that adding Milian and the Netherlands would prove more costly in a distraction and having to defend them than what they brought in with financing. This assessment in fact would have been correct, but it is unrealistic to see someone making it in 1559.
A better POD might be at the end of Felipe II's reign. By this time the Dutch revolt had happened and the Netherlands was becoming a quagmire. Castille had expanded its overseas holdings, not least including the Philippines, and the Spanish Habsburgs had absorbed Portugal. In the seventeenth century maybe one of the Kings of Castile could be persuaded that the empire was overstretched, and that the holdings within the HRE were a logical place to cut back, given they would just go to another branch of the family.