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I too ran into this issue. I'm making a temporary fix in my own fork that just ignores hostname when checking whether a repo matches another given repo, since for us this does not matter.
I think a proper fix has to somehow resolve the hostname to its actual hostname - I looked into this and the only way I can see to do it would be to parse the SSH config file, but that is awful (and there are several files that could set this). There must be a better way, but at this point I'm out of my depth on the solution.