Digital*Ghost,

Chances are that whoever is giving this advice at Ebay doesn't actually understand how the Australian GST works. If, say, they are in the USA, they are probably confusing it with how state sales tax works there - more or less, if a business or reseller has the appropriate tax number for the relevant state, they are not charged the sales tax while all other buyers are.

Ebay Australia probably should consult an Australian accountant to clarify what their obligations are, and actually understand the basics of the law.

Kind Regards,  Kevin