I think it may be easier than you think. Pass a by-law that says owners are responsible for any unauthorized changes to common property, their repair and maintenance and the results of any damage done to common property and personal property as a result of the unauthorized work. The responsibility passes to the next owner if the unit is sold. This by-law doesn’t cancel out the owner’s requirement to inform the EC about and seek permission for changes to common property but it does include common property that has been altered by previous owners.
You would also, obviously, have a by-law covering authorized works with terms and conditions attached.
Of course when I say ‘easier than you think’ this doesn’t take into account a collective desire by owners to get what they can out of an imperfect set of controls.