Hi Sivashanmugam,
It will hit correct GL provided you have configured the following two nodes.
SPRO--->Logistics-General--->Tax on goods movements--->India--->Specify Excise accounts per Excise transaction and Specify GL accounts per excise transaction.
Configure for EWPO transaction.
By this way Part I will be updated in GR document and there will be no issue in taking part II as well.
Regards,
G.Sethuraman