Good point. Actually it is useful in bash scripting when you want to include the output of a command in the arguments of another. However you can get it to work when you press the key twice by using send-prefix like so:

set-option -g prefix `
bind-key ` send-prefix

The only disadvantage is that now you can't copy and paste without losing your backticks, and possibly triggering an action you didn't intend. I haven't yet run into a situation where this was relevant though.