Matt,
The individual binding information you see in the .epf file represents bindings you have introduced yourself, not anything bound by Emacs+.
Binding elements without commandIds is the Eclipse way of un-binding a binding
Often people who come to Emacs+ plus after having tried to set up Emacs-like bindings on their own, without starting from a clean slate, will have a somewhat twisted result. You may want to consider not loading any of your bindings until you have tried Emacs+ and determined what differences from it you require.
There are pages of information about key bindings in Eclipses' help system.
Regards,