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There are added benefits to adding the systems as hosted VMs rather than just a physical machine such as offline patching, template patching, and performing pre-deployment snapshots.
It's very easy to add the machines this way - you just add your VMware host, and then under the 'Hosted Virtual Machines' tab within a machine group, you can enumerate systems on any VMware hosts that have been added.
It's worth trying it out to just add the systems and see if it's easier for you to manage with this method rather than having them added as physical. If you decide to switch over to adding them as virtual in your group, you might as well delete the entries for the machines you had previously added just so that it doesn't attempt to scan the machines twice when you use the machine group. (Even if it did scan a machine twice, one of the two scans would fail as a duplicate scan.)
Let me know if you have any additional questions.