It is evident from the formats provided that government will have stock details with them. However it should be noticed that stock details will be available only up to the point of last return filed and not up to the any given point of time.
However for bigger companies E-way bill will enable government to have near to accurate count of inventory in hand.
Although this will reduce the malpractices of trading in bills but is not full proof.
With time GST will evolve and be able to control such malpractices at larger scale.