Aerial perspective, the "virgin" callsign you refer to is a radio telephony callsign applicable to ATC comms.
The use of "Virgin" by Virgin AMCO on company frequency is not governed by the icao doc and they could call themselves "purple underpants with pink dots" if they wanted to.
Virgin Blue used "Virgin" as a radio telephony callsign for years - 2000 until about 2011 if I remember correctly under an agreement with Airservices. Even with Atlantic operating into Australia - the Atlantic Australian flight numbers were quarantined so there weren't any duplications.
It was only the push to get a common callsign across PB, the 777 operation and the Australian domestic operation that they switched to velocity