For example, to bind C-a to control the remote session:
bind-key -n C-a send-prefixI agree that bindings still don't scale incredibly well depending on the number of host machines you need to ssh from. I think your screen workaround is a pretty neat solution.
If so, I wonder how hard it would be to make tmux into a client of itself using control mode. I only learned about control mode when I discovered iTerm2's tmux integration, whereby remote tmux windows materialize as "actual" terminal windows on my desktop. However, for the same reason that iTerm2 can resize a window, create a new one, show and hide them, etc, I would _imagine_ it's possible to have your remote tmux windows materialize as tmux windows in your local tmux, and thus would be managed using only a single prefix key.
I would guess such a capability would need to be baked into tmux, but I actually wonder how much code would actually be required, since control mode already exists and clearly works quite well.