Hi Jaagrit,
Your latest posting is heading in completely the wrong direction. As your initial posting makes quite clear, your problem is with the Transit area, and nothing to do with Bonded Warehousing.
If you are finding entries in the work-list for creating Declarations prior to Goods Receipt, then the wrong interface is being called by the feeder system. The control is in the configuration for the Inbound Delivery Type - make sure that the flag for the "before GR" is not set.
Regards,
Dave