I think this is close to done. The only annoyance is that you can't add checkbox options while adding a person. I'm not sure it's possible, but if it is, that would be fantastic. I also, don't think there is a need for the single field instrument?
Yes - if you dont need single field instrument, you can edit the post-relationship and remove the field from the intermediary post type.
As the checkboxes field is added to intermediary post type it wont be available on single person or single track edit page. It will be available only on relationship box add/edit.