This does mean a redundant write to the git-annex branch. But,
it means that two clients can be using the same proxy, and after
one sends a file to a proxied remote, the other only has to pull from
the proxy to learn about that. It does not need to pull from every
remote behind the proxy (which it couldn't do anyway as git repo
access is not currently proxied).
Anyway, the overhead of this in git-annex branch writes is no worse
than eg, sending a file to a repository where git-annex assistant
is running, which then sends the file on to a remote, and updates
the git-annex branch then. Indeed, when the assistant also drops
the local copy, that results in more writes to the git-annex branch.