HI Maika
Delivery completed indicator does not stop you to do further GR till you reach the tolerance limit.
Only problem is, once Qty mentioned in PO complete, system set this indicator automatically also for over delivery system does not propose Open GR qty.. so user have manually enter the quantity being received in the Quantity Tab.
Can post the screen shot of error faced by you when you are trying to receive the over delivery within the tolerance limits ?
There is no need to implement any user exit, BADI or configuration change until you already have something in place.
Thanks,
Jagdeep