Potential confusion is of course a safety issue. Pilots must check if they're not sure, don't think anyone would dispute that. The blame for confusion here rests with whoever started it.
Which came first: some atc saying it, some pilots asking every time, some training organisations teaching their pilots they have to ask?
How can the situation be resolved?
I've even heard some pilots readback "cleared for take-off" and follow it up with "can we line up?"
Is this going to be the next step down this wrong road?