It was a defect in VPV 2.20 content pack. If older versions of the content packs are used, the name field was FQDN.
The latest VpV version 1.20 needs to be used which fixed the issue and sent name=shortname.
Download link of the content pack : https://hpln.hpe.com/contentoffering/omi-management-pack-vpv
Then VPV 2.20 will send the shortname for NAME instead of FQDN just like Omi, Sitescope and NNMI other solutions do.
The details was the name attribute should be shortname. With the older CP was shipping name with FQDN instead of shortname causing duplicates.
Resolution is to remove all the nodes with NAME=FQDN and then upgrade to CP 1.20 version. Then the names have no issue.