Why is the account BPRT set as the OWNER of the newly migrated Workstation in Entra?

That is because it is the "Actual user" that Entra Joined the device is using using the Bulk Enrollment Token that is configured on Directories and is used in your Runbook.

Because we can never know for sure the who the "real owner" of a device is we do not  orchestrate changing that.

Intune

When it becomes Intune Enrolled it will show the actual user and that will be in the Intune Portal.  

Change the Owner in Entra

You can change the owner in Entra using the New-MgDeviceRegisteredOwnerByRef graph cmdlet.

Connect to Graph

Connect-MgGraph -Scopes "Device.ReadWrite.All","User.Read.all","Directory.AccessAsUser.All"

Find the device

Make sure you only return one device.

Get-MgDevice -Filter "startswith(displayName,'your device name') and TrustType eq 'AzureAD'"

Add this device to a variable, and collect the current owner from the device

$device = Get-MgDevice -Filter "startswith(displayName,'your device name') and TrustType eq 'AzureAD'"

$CurrentOwner = Get-MgDeviceRegisteredOwner -DeviceId $device.id

Remove the current owner from the device

Remove-MgDeviceRegisteredOwnerByRef -DeviceId $device.id -DirectoryObjectId $CurrentOwner.id

Add the real Owner

Find the desired new owner

Get-MgUser -UserId <the users UPN>

Now register the user on the device

$NewOwner=Get-MgUser -UserId <the users UPN>

New-MgDeviceRegisteredOwnerByRef -DeviceId $device.id -OdataId "https://graph.microsoft.com/v1.0/directoryObjects/$($NewOwner.id)"

Now you can see that the Owner is set correctly.