@Nguyen, Jonathan You can query the SCOM version with Azure Script Extension or with Azure Automation. To get the SCOM Server Version, just execute this PowerShell-Code:
$SCOMVersion = Get-ScomManagementServer | Select-Object Version
You can then assign the version as a tag to the resource.
# Read existing tags
$tags = (Get-AzureRmResource -ResourceGroupName MyResourceGroup -ResourceType Microsoft.Compute/virtualMachines -Name MyVMName).Tags
# Define new tag
$tags += @{Name="SCOMVersion";Value="$($SCOMVersion.Value)"}
# Set the new tag
Set-AzureRmResource -ResourceGroupName MyResourceGroup -Name MyVMName -ResourceType "Microsoft.Compute/VirtualMachines" -Tag $tags