The new version of Prodigy will unify the training workflow so you won't have to specify --binary anymore. However, we still need a small update in spaCy to properly allow updating the components with the respective contstraints defined in the binary feedback, so the results are currently expected to be worse in the nightly. Also see my comment here:
Edit: Just released a new nightly with better support from updating from binary annotations and a fix for the bug mentioned above.