Update Praefect virtual_storages format in ref architectures

What does this MR do?

This is different than the format in the Praefect docs (step 6) which should be used, this MR updates the format from the old, deprecated one, to the new one including 'nodes'.

Related issues

Background in internal Slack thread but essentially, I've asked which format should be used, and @samihiltunen replied:

The format in the ref architectures docs is deprecated and should print out a warning when it’s used. There’s fallback code to handle the old format still. The old format didn’t really match the structure of Praefect’s config and made it awkward to add virtual storage scoped configuration keys as the nodes and other keys would be mixed

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