Interesting that you bring this up. When I originally was prototyping the plugin, I has it so you could add a meta box to multiple post types.
It was confusing the less technical people I was using to help test, and they suggested making it only link to one.
Unfortunately, I rewrote the code to assume only 1 connection, so it's not exactly something I can just turn on.
What would you think about a 'Copy existing meta box' option. Obviously that still leaves the problem of needing to edit multiple meta boxes if they have to change, but at least it would make setting them up easier?
Let me know your thoughts