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I don't know the exact reason for this, but I think it might be related to the fact that during an OVF/IVA deployment, parameters can only be entered if the deployment process is initiated from an existing vCenter Server (i.e. not from en ESXi host). IMO the current deployment process simply provides a wrapper to successfully deploy the vCSA, independent of whether it's done in a new or an existing environment. If you take a look at the installation image's contents, you'll find the .ova file (without a file extension). Other VMware products are still shipped in an OVF/OVA, so I'm sure this format will remain a supported format.
Yes, you are right. The vmware-vcsa file still has OVF and vmdk file. Your reason also make sense because 6.0 Appliance installation just asked me for the host where I want to deploy it and didn't mention vCenter Server anywhere.