Using the Qubes Update tool (or its command-line equivalents), as described here:
I don’t know what that means. My best guess is that it just means to route updates through sys-whonix
(Tor) rather than directly through sys-firewall
(clearnet). Using onion repos is a separate matter.
Again, I don’t know what was intended, but my guess is that you’re correct. To be honest, I don’t know why that’s stated in bold on that page. It seems misplaced (and, as you point out, inaccurate, since you would not be using a Whonix template to update, but rather sys-whonix
).