It looks like this is https://github.com/libgit2/libgit2/issues/6612

And one of the comments on that issue from the libgit2 maintainer made
me realize there's a workaround. Using github.com as an example since
the initial report was having trouble with a channel on github, if you
run this:

$ ssh-keyscan github.com >> ~/.ssh/known_hosts

...it seems to fix the issue, because ssh-keyscan fetches host keys of
all types from the remote host, rather than just one (as seems to
happen when you connect to a remote host via SSH normally).

Obviously would prefer a proper fix, but this is a relatively low-
impact workaround for now.