Various details of the partition in the 1550s were more or less negotiable and no doubt were negotiated quite intensely. But at least one detail was not negotiable.
Why did Ferdinand become emperor after Charles V?
Charles V was elected emperor on 28 June 1519 and crowned King of the Romans on 26 October 1520. He was crowned King of Italy on 22 February 1530 and crowned Emperor of the Romans on 24 February 1530.
For various reasons the seven electors met and agreed to make Ferdinand the next emperor. He was elected King of the Romans and future emperor on 5 January 1531. This made it inevitable that he would be the next emperor (barring revolution of some type or premature death). He was crowned King of the Romans at Aachen on 11 February 1531.
In September 1556 Charles V abdicated as Holy Roman Emperor in favor of Ferdinand, King of the Romans. On 24 February 1558 the electors met and formally accepted the abdication, thus making Ferdinand the emperor with full imperial powers. Ferdinand was crowned Emperor elect of the Romans at Frankfurt on 14 march 1558.
So the main question why Ferdinand became Emperor of the Romans in 1558 was why the electors considered the advantages of electing him King of the Romans in 1531 out weighed any disadvantages they might have seen in the process. Once Ferdinand was elected King of the Romans in 1531 he was legally the next emperor and only some sort of revolution, or predeceasing Charles V, could have prevented him from being the next emperor.
Ferdinand becoming emperor was not decided in any family meetings to divide the Habsburg lands in the 1550s. It had already been decided by the seven electors in 1531 that Ferdinand would automatically become the next emperor when Charles V ceased to reign as emperor.
The Habsburgs could have decided to divide up their various kingdoms and duchies and other lands in any of an almost infinite number of ways in the 1550s, and in my opinion it would have been better to give more lands to the next emperor - for example by giving the Netherlands, Milan, and the kingdoms of the Crown of Aragon to whichever member of the family would be the next emperor. But the question of who would be the next emperor was a matter that had already been decided 2 decades earlier in a meeting of the electors.