When you re-registered the VM with the SQL IaaS Agent Extension, did you perform the delete of the SQL VM resource (NOT the VM) and then re-create? It should have detected the version at the time of creating the SQL VM resource.
You can check what the SQL IaaS Agent Extension found by looking in:
*C:\Packages\Plugins\Microsoft.SqlServer.Management.SqlIaaSAgent<latest version>\Status*
From a billing perspective, the version does not make a difference - it is the edition that matters.