We have enabled user based License for VPP Apps and enabled auto update option in Apple VPP token.
As per the MS Document User based license will take local App store settings configuration. That cannot be managed by the Intune admin.
But Now also VPP applications are getting updated automatically over Mobile Data even when the user licensing has been set in the assignment and Mobile Data is disabled in Automatic Downloads within the device settings. Below article was followed.
How to manage iOS and macOS apps purchased through Apple Volume Purchase Program with Microsoft Intune: https://docs.microsoft.com/en-us/mem/intune/apps/vpp-apps-ios.
So suggest how to stop autoupdates happening through mobile data.