Please see this thread which outlines the conditions required for the system level and course category level question banks to be included in a course backup: https://moodle.org/mod/forum/discuss.php?d=377855.
If quizzes are dependent upon questions in the system or course category question bank those need to be included in the course backup if the course is going to be restored to another instance of Moodle. However, when a user is manually creating a course backup it would be helpful to provide control over whether or not to include the system or course category question bank. If the user knows how the backup is going to be used, they should have the opportunity to make an educated choice to include or exclude the system and course category question banks. It would be best if such functionality were accompanied with a warning about potential impact on quizzes of excluding these question banks.
Also, I would envision this option only applying to the question banks as they are needed. In other words, if the quizzes in the course are not dependent upon the system question bank, do not give the user the option to choose to include the system question bank. Or if availability of the checkbox cannot be controlled in this fashion at least interpret the selection of the "Include system question bank" checkbox to mean only include it as needed by the quizzes in the course.
If these options are added to the course backup wizard then corresponding settings should probably be added to General backup defaults.