It does require some gyrations to get around the fact that it logs everything (the command itself, terminal control, etc), and not just what's output by the command. Here's a quick and dirty example:

a) Start a tmux session to a remote host

b) On the local host, run this (assuming session 0):

$ tmux pipe-pane -o -t0 "tail -n +2 | col -b | base64 -d > ~/output"

$ tmux send-keys -t0 "base64 /some/file && read" Enter

$ tmux pipe-pane -t0

$ tmux send-keys -t0 Enter

You should now have ~/output on the local host, which is identical to /some/file on the remote.