As of now submitted GST application seems to be locked and amendments is not allowed but it will be unlocked after few days!!!
One point to note is that GST is not implemented, so legally you are safe. Anyhow GST number will be PAN based and whether you register with VAT or service tax provision id, it should not matter.
For more we have to wait for announcement by GST department.
chatCommentsIts look logical that there be no issue even if service tax number is not provided. For instance, if someone got service tax number post GST migration with VAT provison id. - GST Payer