What if instead of OTL's partition, he deeded Spain, Naples, Austria, Bohemia and Hungary to Philip and the Burgundian inheritance and Milan to Ferdinand, while also supporting Ferdinand for HRE?
How does Ferdinand handle the Netherlands and Milan?
How does European history change with Spain under Spain probably not involved in the Netherlands Revolt and northern Italy, but possibly more involved with trying to defend and extend Hungary and Croatia?
Charles had no authority/right over Bohemia (except as HRE) and Hungary. Bohemia & Hungary were inherited by Ferdinand by right of marriage to his wife Anna and as such were Ferdinand & Anna's so Charles couldn't give it to Philip.
Austria was given to Ferdinand because of Maximilian I will and to appease the estates of Bohemia and Hungary around the time Ferdinand married Anna in 1521 (he was governor of Austria on Charles's behalf but I think they'd pretty much decided he'd get something there).
Only parts Charles can conceivably divide are Milan & the Burgundian inheritance. If all goes OTL, but Ferdinand gets both or they are given to Maria of Spain when she marries Maximilian II it'd be great. Not saying no Dutch revolt (the region had one reason or another, not to be dismissive, to revolt agx the Habsburgs especially due to their centralising ways from Maximilian I as regent, to Charles V on taxes) but it'd be a heck of a lot easier to manage.
If Ferdinand gets it
Maximilian - Austria + Bohemia + Hungary
Ferdinand (of further Austria) - might get the low countries but his morganatic marriage may be an issue, or else an understanding is made and the low countries revert to Maximilian II on his death.
Charles of Styria - Milan.
Most of Ferdinand's sons to some degree were accomodating of Protestantism, not sure of Ferdinand of further austria because the reformation didn't really penetrate there as far as I'm aware. Maximilian we know was so inclined that Ferdinand I had to promise the pope that Maximilian wouldn't succeed him as Emperor if Maximilian converted. Charles of Styria while introducing the counter-reformation still made a deal with the Protestant nobility in Styria granting them some rights.
Now if it goes to Maximilian II, even better. Not only do we completely side step the religious aspect of the revolt during his era. When he divides his realms as he likely will. We have so many sons to choose
Rudolf II - Austria + Bohemia + Hungary
Ernest - Low countries/ 17 provinces
Matthias - Milan
Albert - can get further Austria if Ferdinand of further Austria doesn't marry
Wenceslaus - maybe make him Landgrave of Sundgau and Free count of Burgundy.
Morganatic sons of Ferdinand of further Austria get sent to cozy positions in the church, maybe prince bishop of Liege. Archbishop of Toledo.
Effects of HRE:
Stronger powerbase for the Emperor. Possibly actual threat of enforcement of who's realm who's religion and preservation of the petty prince-bisphorics rather than them being secularised by protestant princes in violation of the peace of Augsburg. The 17 provinces will revolt but it likely won't turn into the mess it was OTL. More resources for the reconquest of Hungary and Croatia. Not saying Austria will win be she'll definitely give the Ottomans a greater run for their money.
France, if the HRE & Spain are not directly attached her encroachment in the Rhine won't go over as well. I see her focusing on Italy specifically Savoy and on Navarre in the Iberian peninsula. France will probably attempt a detente will England (they'll play the region agx each other as always, perfidious Albion). I don't think the wars will go as well for France as the relative new branches can focus on their goals and defence well enough. Resources will not be as spread thin.