Please be aware that the auto body repair shop must follow the process set forth by the insurance company who is managing your auto body repair claim. Whether an insurance adjuster wrote your original estimate or the body shop wrote your original estimate the insurance company will typically not allow them to write for unseen/hidden damage even if more damage is suspected. This means that the person writing the estimate can only write for damage they can actually see and take photos of. If the vehicle is drive-able at the time the estimate is written then the vehicle will not be torn down to assess for further damage until it is actually dropped off at the shop for the repair. This allows you to continue driving the vehicle until your repair can be scheduled.
This is why it is not uncommon for an auto body shop to report supplemental damage once a vehicle is dropped off for repair and has the opportunity to tear the vehicle down. This allows the estimator to see the previously hidden damage take photos and report it to the insurance company. At this point the insurance company will either give the approval to move forward with the repair or in some cases they may want to come out and review the additional damage them selves. Be aware that additional damage may increase the cost of the repair and can also extend the time it takes to complete the repair. The insurance company will cover the additional damage if it is related to the accident and if you are in a rental they will typically extended the rental to cover the additional time it may take to fix the supplemental damage found. Your auto body shop should have an open line of communication with you and the insurance company keeping you both fully informed.