I don't see the situation being wholly different than Ferdinand I's reign to begin with but remember that Charles V was accepted because he was "one of them", and that he relativly let them free to do as they pleased.
With the ongoing war with Turks, centralizing reforms, still ingoing Reformation and huge fiscal needs for all of that, and a more close imperial presence (so less room to go against imperial wishes), it's not going to change radically favourably.
Considering that there wasn't a second living son IOTL, the safest is to assume this son would be quite akin to Philipp II.
On this, the traditional criticism of being a "fanatic" have to be really nuanced. It's part of the dark legend of Spain, depicted as a nest of vicious priests-kings.
Religion, whatever for Catholics or Protestants, was a political and ideological weapon, and fighting against the rival was a political necessity for both side (hence the Union of Arras creation).
The second son, critically if inheriting the HRE, would necesserily defend Catholicism against Protestantism would it be only for the sake of its own legitimacy.