Flying out of Hobart, whenever its Qantas, its nearly always QantasLink. And I'm perfectly happy with that/them. I'm really looking forward to the A220s as I slide my backside back into QF (QFL) upholstery.
But I do join your wonder why they keep the distinction up. I know there is ownership and licencing history but can't see it. Unless (as you speculated) - its cost. Maybe QantasLink employees have historically been on poorer wage agreements and it suits the company to keep it up?
QLink are on substantially less than mainline counterparts and unlike airlines in the US/Europe there are no scope clauses for QF hence more and more flying being taken over by lower cost subsidiaries