The fee is charged to the student, not the society, and is paid to the Arc, not the society. Societies may optionally choose to have their own sign-up fee, which in the past have tended to be less than $10 for most clubs.
The $40 fee applies to joining clubs which are affiliated with the Arc. Clubs can choose not affiliate with the Arc, however they then miss out on many of the free services and resources which the Arc provide (such as free room hire and bookings, stalls at O-Week and other events, etc) to help out the clubs. For these clubs, the only fee the student must pay is the membership fee for the club itself.
The so called constituent clubs, which are affiliated with faculties (or schools), (to the best of my knowledge) draw their membership directly from the faculty (or school), so any student enrolled in said faculty or school is automatically a member of this club, and do not need to pay the Arc administration fee (or be a member of the Arc). The resources which Arc clubs rely on are then provided by the school or faculty in question.
The final terms and conditions of Arc membership have not been made official yet (they will be available before O-Week) so everything mentioned here should be considered provisional. You should check the Arc website closer to O-Week for the full, official details regarding all forms of club membership.