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What is the benefit of building the same website twice with different hostnames instead of using relative links to content on the same domain?

Fair point. Very small things like RSS, canonical link or og:url or microformats use absolute URL

To make sure once in the .onion, you never leave the .onion

Website impersonation/fronting is a big problem in onionland, this at least makes fronters need to take more effort.

Not enough to be worth it.