Charles V was certainly a man of ambition and one of his ambitions was to unify and centralise his dominions - and more specifically, the Low Countries. This should be seen in the wider context of centralising states and the emerging bureaucracy, two phenomena that were gaining traction in Europe around that time. Both resulted in more control to the central ruler and more efficiency in general. To reach this centralised reality, Charles had taken a few measures already - conquering or receiving areas like Gelre, Groningen and Friesland, forcing Francis I of France to relinquish his rights to parts of the Netherlands and creating clarity with regards to the the status of the Netherlands vis a vis the HRE with the Transaction of Augsburg a year earlier. This last act created the Burgundian Kreits and essentially declared the Netherlandish territories as an administrative whole.

Now, up until that point, Charles had basically been ruler of every little city, province, duchy, and so on, but he had no unifying title in the Netherlands. The Netherlands might have been an administrative whole, but his lack of a unifying title was a last stumbling block to a centralised state and to removing the medieval customs. So, with the Pragmatic Sanction, he declared the Netherlands an in-dividable whole, with him in charge of course.

Let's look deeper into the reason why he did this. He issued the Sanction to aid his centralisation of the Netherlands, but why did he want to centralise the area? This question has a few answers, some of which I've touched on already: efficiency, for instance. A centralised state in this context is much more efficient - and profitable - than what came before. But it was also about control and power, of course. While the various states, cities and the guilds weren't really that much of a threat anymore - not after the bloody suppression of Den Bosch in 1525, Utrecht in 1528 and the Revolt of Ghent in 1539. I also recall that he literally wiped a city in the Netherlands off the face of the earth, but perhaps appropriately, I can't recall its name. Anyway, these threats were essentially neutered, but with the Sanction came a more firm legal setting for Charles. On top of this, by centralising and forming a bureaucracy, Charles no longer had to rely on old noble families as much - as the administration of his empire could now be delegated to men loyal to him - or more exactly, to his coin. The whole affair also put him in a better position to deal with the ongoing Reformation, I think.

Now, of course, the Sanction also helped keep the area in Habsburg hands. Succession rights are incredibly complicated and are one of the prime reasons why Charles ended up ruling over such a great empire - an empire he was prophesied to get by means of Venus, not Mars. So I'm sure he was aware of the risk of fragmentation and the loss of territories. He must've considered what ended up happening to Charlemagne's empire - divided up between his sons and ultimately broken into a thousand pieces. But a single entity can't easily be broken up (except, y'know, if one part revolts - sorry for the spoilers), so unifying the titles made sense.

As to the (sort of ironic) split after Charles' rule - I think he knew it would happen when he signed the Sanction. After all, Ferdinand I had been ruling his Austrian lands for ages and had been declared Roman King back in 1531, meaning he was the heir to the HRE. I'm not really sure about this part of your question, but I can imagine you're right about it playing a part in his decision. It probably would've been easier for Ferdinand to claim parts of the Netherlands - particularly the parts under the Westfalian Kreits - if it wasn't unified. Then again, it was probably clear from early on that Ferdinand would only get the Austrian heartlands - after all, areas like the dominions in Italy which were even closer and more linked to the Austrian lands weren't handed over to him either.

Hope this helped a bit.