You still need to quote the command though. `hyperfine -N ls "$dir"' won't work, you need `hyperfine -N "ls ${dir@Q}"' or something. It'd be better if you could specify commands like with `find -exec'.
hyperfine -N -- ls "$dir" \; my_ls "$dir"Looks fine to me. Obviously it's too late to undo that mistake, but a new flag to enable new behavior wouldn't hurt anyone.