Nothing has changed with the default directory structure. Such a change would break so many things it is hardly worth doing:)
That said, you can change the logic responsible for where to store entries by extending the kPathManager class defined here /opt/kaltura/app/alpha/apps/kaltura/lib/storage/kPathManager.php.
There are also these two classes:
You can create additional 'local' storages [the word local is a bit confusing because /opt/kaltura/web can, and in the event of cluster ENV, should, be mounted from a remote storage device using NFS but in this context, local means, as opposed to some external CDN] by going to Admin Console->Publishers->Your partner->Profiles->Remote Storage, selecting 'Local' as protocol and selecting a different "Path Manager" under "Export Details".
Of course, you'll also need to consider the delivery profiles, as well. For a more detailed explanation about the relationship between them, see:
As a general rule, I recommend making such changes very carefully as these are 2 core system functionalities and failure in either one will make the system malfunction. Such changes should never be tested directly on your production ENV.
Hope that helps,