To echo what I think Janprimus is saying, I don't see how you keep Austria and Bohemia from going to Ferdinand. These were not part of the inheritance for Charles V. They were elected monarchies, and elected Ferdinand, who married into the royal families of these monarchies. And if he gets them, it makes sense for him to get the Austrian duchies.
The swing crowns in any division are the imperial title, the Netherlands, and Lombardy. The imperial title is also elective and I just can't see the Electors preferring Philip to Ferdinand. This did lead to the anomaly that the less powerful branch of the Habsburgs wound up with the imperial title. Since the Netherlands and Lombardy were within the boundaries of the Holy Roman Empire, it would have made sense to give them to the Austrian branch. There were various proposals later to do something like this with the Netherlands to try to resolve the war there, and both the Netherlands (part of it) and Lombardy wound up with the Austrian branch eventually. This division would have made more sense, especially as Philip wound up getting Portugal. However, this requires more hindsight than is really possible, they didn't know that the Spanish branch would absorb Portugal or be unable to maintain control over the Netherlands.
Also, division among family members historically has been the standard method of handling large collections of crowns such as the Hapsburg inheritance. The surprising thing is that Philip wound up with so much of it.